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Metabolites
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Harnessing Primary and Secondary Plant Metabolite Information for Biotechnologically Derived...
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Harnessing Primary and Secondary Plant Metabolite Information for Biotechnologically Derived Bioproducts

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: closed (15 January 2021) | Viewed by 8702

Special Issue Editors

Dr. Edward Baidoo

E-Mail Website
Guest Editor
Lawrence Berkeley National Laboratory, Emeryville, CA, USA
Interests: metabolomics; metabolism; data analysis; data interpretation
Dr. Aymerick Eudes

E-Mail Website
Guest Editor
Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
Interests: crop engineering; secondary metabolism; lignin; bioproducts
Dr. Bashar Amer

E-Mail Website
Guest Editor
Lawrence Berkeley National Laboratory, Emeryville, CA, USA
Interests: metabolomics; data analysis

Special Issue Information

Dear Colleagues,

The production of plant-based bioproducts through biotechnology routes is becoming increasingly important to the biofuel, pharmaceutical, fiber, cosmetic, fragrance, food, and flavor industries. Most of these biochemical products are derived from primary and secondary plant metabolism, where the former provides energy and building blocks for the latter. Plant metabolism can be rewired by various genetic engineering approaches to improve bioproduct yield and adaptation to biotic and abiotic environmental stresses. Plant metabolic engineering, however, does not always produce the desired outcome, as the flow of biochemical information is multidirectional via complex interactions between the genome, proteome, transcriptome, and metabolome. In this regard, the analysis of the metabolome (i.e., metabolomics) plays a key role in the provision of metabolic information as it enables the correlation of gene expression to phenotypic (i.e., metabolite) information. Furthermore, metabolomics can be used to quantify and qualify plant bioproducts, identify bottlenecks in engineered pathways via the quantitation of pathway intermediates and cofactors, and assess the impact of an engineered pathway on plant metabolism and agronomical performance.

This Special Issue will highlight the use of primary and secondary plant metabolite information for biotechnologically derived bioproducts. Authors are invited to submit original articles and well-documented reviews related, but not limited, to the identification and/or quantitation of metabolites/bioactive compounds with biological and/or clinical relevance (possibly in relation to biotechnologically derived bioproducts) and metabolomics and descriptions of new plant-derived bioproducts and biomarkers of metabolism.

Dr. Edward Baidoo
Dr. Aymerick Eudes
Dr. Bashar Amer
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. Metabolites 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.

Keywords

  • Plants
  • Bioproducts
  • Metabolites
  • Metabolomics
  • Metabolic engineering

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Published Papers (3 papers)

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Research

17 pages, 7937 KiB  
Article
Downregulation of Squalene Synthase Broadly Impacts Isoprenoid Biosynthesis in Guayule
by Dante Placido, Niu Dong, Bashar Amer, Chen Dong, Grisel Ponciano, Talwinder Kahlon, Maureen Whalen, Edward E. K. Baidoo and Colleen McMahan
Metabolites 2022, 12(4), 303; https://doi.org/10.3390/metabo12040303 - 29 Mar 2022
Cited by 4 | Viewed by 2449
Abstract
Production of natural rubber by Parthenium argentaum (guayule) requires increased yield for economic sustainability. An RNAi gene silencing strategy was used to engineer isoprenoid biosynthesis by downregulation of squalene synthase (SQS), such that the pool of farnesyl diphosphate (FPP) substrate might instead be [...] Read more.
Production of natural rubber by Parthenium argentaum (guayule) requires increased yield for economic sustainability. An RNAi gene silencing strategy was used to engineer isoprenoid biosynthesis by downregulation of squalene synthase (SQS), such that the pool of farnesyl diphosphate (FPP) substrate might instead be available to initiate natural rubber synthesis. Downregulation of SQS resulted in significantly reduced squalene and slightly increased rubber, but not in the same tissues nor to the same extent, partially due to an apparent negative feedback regulatory mechanism that downregulated mevalonate pathway isoprenoid production, presumably associated with excess geranyl pyrophosphate levels. A detailed metabolomics analysis of isoprenoid production in guayule revealed significant differences in metabolism in different tissues, including in active mevalonate and methylerythritol phosphate pathways in stem tissue, where rubber and squalene accumulate. New insights and strategies for engineering isoprenoid production in guayule were identified. Full article
(This article belongs to the Special Issue Harnessing Primary and Secondary Plant Metabolite Information for Biotechnologically Derived Bioproducts)
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12 pages, 12340 KiB  
Article
The Interface amongst Conserved and Specialized Pathways in Non-Paclitaxel and Paclitaxel Accumulating Taxus Cultures
by Michelle C. McKee, Sarah A. Wilson and Susan C. Roberts
Metabolites 2021, 11(10), 688; https://doi.org/10.3390/metabo11100688 - 7 Oct 2021
Cited by 3 | Viewed by 2028
Abstract
Plant cell cultures derived from Taxus are used to produce valuable metabolites like paclitaxel, a chemotherapeutic drug. Methyl jasmonate elicitation enhances paclitaxel accumulation, but also inhibits culture growth and increases phenylpropanoid biosynthesis, two side effects that detract from taxane accumulation. To understand the [...] Read more.
Plant cell cultures derived from Taxus are used to produce valuable metabolites like paclitaxel, a chemotherapeutic drug. Methyl jasmonate elicitation enhances paclitaxel accumulation, but also inhibits culture growth and increases phenylpropanoid biosynthesis, two side effects that detract from taxane accumulation. To understand the connection between all of these processes, a systems approach is applied to investigate cell-wide metabolism in Taxus. Non-paclitaxel and paclitaxel accumulating cultures were elicited over single and multi-generational periods, and subsequent changes in conserved and specialized metabolism were quantified. Methyl jasmonate typically resulted in decreased growth and increased metabolite content in paclitaxel accumulating cultures. Conversely, elicitation typically resulted in either no change or decrease in accumulation of metabolites in the non-paclitaxel accumulating cultures. In both sets of cultures, variability was seen in the response to methyl jasmonate across generations of cell growth. Consolidation of these data determined that paclitaxel accumulation and basal levels of phenolic and flavonoid compounds are indirectly correlated with aggregate size. These approaches assess alternative metabolic pathways that are linked to paclitaxel biosynthesis and provide a comprehensive strategy to both understand the relationship between conserved and specialized metabolism in plants and in the design of strategies to increase natural product yields in plant cell culture. Full article
(This article belongs to the Special Issue Harnessing Primary and Secondary Plant Metabolite Information for Biotechnologically Derived Bioproducts)
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15 pages, 1413 KiB  
Article
Developing a Yeast Platform Strain for an Enhanced Taxadiene Biosynthesis by CRISPR/Cas9
by Joseph C. Utomo, Fabio C. Chaves, Philippe Bauchart, Vincent J. J. Martin and Dae-Kyun Ro
Metabolites 2021, 11(3), 147; https://doi.org/10.3390/metabo11030147 - 3 Mar 2021
Cited by 5 | Viewed by 3575
Abstract
Paclitaxel is an important diterpenoid commonly used as an anticancer drug. Although the paclitaxel biosynthetic pathway has been mostly revealed, some steps remain to be elucidated. The difficulties in plant transformations and the scarcity of the precursor of paclitaxel, (+)-taxa-4(5), 11(12)-diene (taxadiene), have [...] Read more.
Paclitaxel is an important diterpenoid commonly used as an anticancer drug. Although the paclitaxel biosynthetic pathway has been mostly revealed, some steps remain to be elucidated. The difficulties in plant transformations and the scarcity of the precursor of paclitaxel, (+)-taxa-4(5), 11(12)-diene (taxadiene), have hindered the full comprehension of paclitaxel biochemistry and, therefore, its production by biotechnological approaches. One solution is to use the budding yeast, Saccharomyces cerevisiae, as a platform to elucidate the paclitaxel biosynthesis. As taxadiene is a diterpenoid, its common precursor, geranylgeranyl pyrophosphate (GGPP), needs to be increased in yeast. In this study, we screened various GGPP synthases (GGPPS) to find the most suitable GGPPS for taxadiene production in yeast. We also optimized the taxadiene production by increasing the flux toward the terpenoid pathway. Finally, to remove selection markers, we integrated the required genes using a CRISPR/Cas9 system in the yeast genome. Our result showed that a titer of 2.02 ± 0.40 mg/L (plasmid) and 0.41 ± 0.06 mg/L (integrated) can be achieved using these strategies. This platform strain can be used to readily test the gene candidates for microbial paclitaxel biosynthesis in the future. Full article
(This article belongs to the Special Issue Harnessing Primary and Secondary Plant Metabolite Information for Biotechnologically Derived Bioproducts)
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