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Biomolecules
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Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches...
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Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches and Mechanistic Insights

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Cellular Biochemistry".

Deadline for manuscript submissions: closed (15 August 2021) | Viewed by 29751

Special Issue Editors

Dr. Roque Bru-Martinez

E-Mail Website
Guest Editor
Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Research Ramon Margalef, University of Alicante, 03690 Alicante, Spain
Interests: stilbenoids synthesis and trafficking; phenylpropanoids; metabolic engineering; plant cell culture; grapevine; elicitor signaling
Dr. Giulia Malacarne

E-Mail Website
Guest Editor
Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre - Fondazione Edmund Mach, San Michele all'Adige (Trento), Italy
Interests: grapevine functional genomics; transcriptional regulation of secondary metabolism; gene regulatory networks; quality of fruit; response to biotic stresses mediated by phenylpropanoids
Dr. José Tomás Matus

E-Mail Website
Guest Editor
Institute for Integrative Systems Biology (I2SysBio, Universitat de València-CSIC), Valencia, Spain
Interests: phytopharmaceuticals; transcription factors; systems biology; multi-omics integration; gene regulatory networks; phenylpropanoids; isoprenoids; fleshy fruits; cannabinoids

Special Issue Information

Dear Colleagues,

Plants produce a myriad of specialized (secondary) metabolites with a multitude of biological roles such as conferring light/UV protection, providing color patterns as visual aids for pollination or seed dispersal, regulating plant development, and being part of pathogen defense responses. Aside from these roles, specialized metabolites are of major interest for human nutrition and health. The major pathways of secondary metabolism are those producing isoprenoids, phenylpropanoids, alkaloids, and polyketides. The comprehension of their biosynthesis and regulation has acquired major advances mostly nurtured from reverse and forward genetics approaches in several plant species, which have given access to both structural and regulatory genes of these pathways. This knowledge has been particularly relevant for establishing strategies for breeding and altering metabolite content in crops or engineering plants used for biofuels. However, major advances have only been addressed for conserved pathways across the plant kingdom and those restricted to certain species have been somehow less studied. We also still lack information on how these pathways are precisely fine-tuned, how the metabolites are conjugated, transported and accumulated, or how different specialized metabolisms may compete for carbon-flux or uptake of primary metabolites. The understanding of these mechanisms should benefit from a multidisciplinary approach involving strong computational analyses of big data being currently generated. This Special Issue welcomes the submission of scientific articles focused on the deciphering of the fine regulation of specialized metabolism in different plant species by using different approaches, including the integration of multi-omics data. We especially welcome experimental studies proving mechanistic insights into how specialized metabolites are being tightly regulated, including compartmentalization. Studies in crops, model species, and plant cell culture models will be considered, as well as fully-computational studies not necessarily involving experimental activities. Reviews or Articles are also welcome.

Note: For experimental studies involving omics data analyses it is mandatory that they include at least three biological replicates.

Dr. Roque Bru-Martinez
Dr. Giulia Malacarne
Dr. José Tomás Matus
Guest Editors

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. Biomolecules is an international peer-reviewed open access monthly 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.

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Published Papers (5 papers)

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Research

Jump to: Review

19 pages, 5080 KiB  
Article
Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families
by Stefania Pilati, Giulia Malacarne, David Navarro-Payá, Gabriele Tomè, Laura Riscica, Valter Cavecchia, José Tomás Matus, Claudio Moser and Enrico Blanzieri
Biomolecules 2021, 11(12), 1744; https://doi.org/10.3390/biom11121744 - 23 Nov 2021
Cited by 16 | Viewed by 4427
Abstract
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof [...] Read more.
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs. Full article
(This article belongs to the Special Issue Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches and Mechanistic Insights)
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18 pages, 1888 KiB  
Article
Down-Regulation of Phosphoenolpyruvate Carboxylase Kinase in Grapevine Cell Cultures and Leaves Is Linked to Enhanced Resveratrol Biosynthesis
by Elías Hurtado-Gaitán, Susana Sellés-Marchart, James Hartwell, Maria José Martínez-Esteso and Roque Bru-Martínez
Biomolecules 2021, 11(11), 1641; https://doi.org/10.3390/biom11111641 - 5 Nov 2021
Cited by 7 | Viewed by 2122
Abstract
In grapevine, trans-Resveratrol (tR) is produced as a defence mechanism against stress or infection. tR is also considered to be important for human health, which increases its interest to the scientific community. Transcriptomic analysis in grapevine cell cultures treated with the defence response [...] Read more.
In grapevine, trans-Resveratrol (tR) is produced as a defence mechanism against stress or infection. tR is also considered to be important for human health, which increases its interest to the scientific community. Transcriptomic analysis in grapevine cell cultures treated with the defence response elicitor methyl-β-cyclodextrin (CD) revealed that both copies of PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) were down-regulated significantly. A role for PPCK in the defence response pathway has not been proposed previously. We therefore analysed the control of PPCK transcript levels in grapevine cell cultures and leaves elicited with CD. Moreover, phosphoenolpyruvate carboxylase (PPC), stilbene synthase (STS), and the transcription factors MYB14 and WRKY24, which are involved in the activation of STS transcription, were also analysed by RT-qPCR. The results revealed that under CD elicitation conditions PPCK down-regulation, increased stilbene production and loss of PPC activity occurs in both tissues. Moreover, STS transcripts were co-induced with MYB14 and WRKY24 in cell cultures and leaves. These genes have not previously been reported to respond to CD in grape leaves. Our findings thus support the hypothesis that PPCK is involved in diverting metabolism towards stilbene biosynthesis, both for in vitro cell culture and whole leaves. We thus provide new evidence for PEP being redirected between primary and secondary metabolism to support tR production and the stress response. Full article
(This article belongs to the Special Issue Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches and Mechanistic Insights)
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Review

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21 pages, 3362 KiB  
Review
Transcription Factors in Alkaloid Engineering
by Yasuyuki Yamada and Fumihiko Sato
Biomolecules 2021, 11(11), 1719; https://doi.org/10.3390/biom11111719 - 18 Nov 2021
Cited by 18 | Viewed by 3850
Abstract
Plants produce a large variety of low-molecular-weight and specialized secondary compounds. Among them, nitrogen-containing alkaloids are the most biologically active and are often used in the pharmaceutical industry. Although alkaloid chemistry has been intensively investigated, characterization of alkaloid biosynthesis, including biosynthetic enzyme genes [...] Read more.
Plants produce a large variety of low-molecular-weight and specialized secondary compounds. Among them, nitrogen-containing alkaloids are the most biologically active and are often used in the pharmaceutical industry. Although alkaloid chemistry has been intensively investigated, characterization of alkaloid biosynthesis, including biosynthetic enzyme genes and their regulation, especially the transcription factors involved, has been relatively delayed, since only a limited number of plant species produce these specific types of alkaloids in a tissue/cell-specific or developmental-specific manner. Recent advances in molecular biology technologies, such as RNA sequencing, co-expression analysis of transcripts and metabolites, and functional characterization of genes using recombinant technology and cutting-edge technology for metabolite identification, have enabled a more detailed characterization of alkaloid pathways. Thus, transcriptional regulation of alkaloid biosynthesis by transcription factors, such as basic helix–loop–helix (bHLH), APETALA2/ethylene-responsive factor (AP2/ERF), and WRKY, is well elucidated. In addition, jasmonate signaling, an important cue in alkaloid biosynthesis, and its cascade, interaction of transcription factors, and post-transcriptional regulation are also characterized and show cell/tissue-specific or developmental regulation. Furthermore, current sequencing technology provides more information on the genome structure of alkaloid-producing plants with large and complex genomes, for genome-wide characterization. Based on the latest information, we discuss the application of transcription factors in alkaloid engineering. Full article
(This article belongs to the Special Issue Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches and Mechanistic Insights)
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14 pages, 1226 KiB  
Review
Effect of Polyploidy Induction on Natural Metabolite Production in Medicinal Plants
by Hadi Madani, Ainoa Escrich, Bahman Hosseini, Raul Sanchez-Muñoz, Abbas Khojasteh and Javier Palazon
Biomolecules 2021, 11(6), 899; https://doi.org/10.3390/biom11060899 - 17 Jun 2021
Cited by 50 | Viewed by 10173
Abstract
Polyploidy plays an important role in plant diversification and speciation. The ploidy level of plants is associated with morphological and biochemical characteristics, and its modification has been used as a strategy to alter the quantitative and qualitative patterns of secondary metabolite production in [...] Read more.
Polyploidy plays an important role in plant diversification and speciation. The ploidy level of plants is associated with morphological and biochemical characteristics, and its modification has been used as a strategy to alter the quantitative and qualitative patterns of secondary metabolite production in different medicinal plants. Polyploidization can be induced by many anti-mitotic agents, among which colchicine, oryzalin, and trifluralin are the most common. Other variables involved in the induction process include the culture media, explant types, and exposure times. Due to the effects of polyploidization on plant growth and development, chromosome doubling has been applied in plant breeding to increase the levels of target compounds and improve morphological characteristics. Prompted by the importance of herbal medicines and the increasing demand for drugs based on plant secondary metabolites, this review presents an overview of how polyploidy can be used to enhance metabolite production in medicinal plants. Full article
(This article belongs to the Special Issue Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches and Mechanistic Insights)
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26 pages, 3016 KiB  
Review
Recent Insights into Anthocyanin Pigmentation, Synthesis, Trafficking, and Regulatory Mechanisms in Rice (Oryza sativa L.) Caryopsis
by Enerand Mackon, Guibeline Charlie Jeazet Dongho Epse Mackon, Yafei Ma, Muhammad Haneef Kashif, Niyaz Ali, Babar Usman and Piqing Liu
Biomolecules 2021, 11(3), 394; https://doi.org/10.3390/biom11030394 - 7 Mar 2021
Cited by 56 | Viewed by 8027
Abstract
Anthocyanins are antioxidants used as natural colorants and are beneficial to human health. Anthocyanins contribute to reactive oxygen species detoxification and sustain plant growth and development under different environmental stresses. They are phenolic compounds that are broadly distributed in nature and are responsible [...] Read more.
Anthocyanins are antioxidants used as natural colorants and are beneficial to human health. Anthocyanins contribute to reactive oxygen species detoxification and sustain plant growth and development under different environmental stresses. They are phenolic compounds that are broadly distributed in nature and are responsible for a wide range of attractive coloration in many plant organs. Anthocyanins are found in various parts of plants such as flowers, leaves, stems, shoots, and grains. Considering their nutritional and health attributes, anthocyanin-enriched rice or pigmented rice cultivars are a possible alternative to reduce malnutrition around the globe. Anthocyanin biosynthesis and storage in rice are complex processes in which several structural and regulatory genes are involved. In recent years, significant progress has been achieved in the molecular and genetic mechanism of anthocyanins, and their synthesis is of great interest to researchers and the scientific community. However, limited studies have reported anthocyanin synthesis, transportation, and environmental conditions that can hinder anthocyanin production in rice. Rice is a staple food around the globe, and further research on anthocyanin in rice warrants more attention. In this review, metabolic and pre-biotic activities, the underlying transportation, and storage mechanisms of anthocyanins in rice are discussed in detail. This review provides potential information for the food industry and clues for rice breeding and genetic engineering of rice. Full article
(This article belongs to the Special Issue Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches and Mechanistic Insights)
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