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Book: Microbial metabolomics

Baidoo, Edward E. K.

methods and protocols

(Methods in molecular biology ; 1859 ; Springer protocols)

2019

Author's details	edited by Edward E.K. Baidoo
Series title	Methods in molecular biology ; 1859 Springer protocols
Collection
Keywords	Mikroorganismus ; Metabolomik
Subject	Keim ; Mikrobe ; Mikroben
Language	English
Size	x, 351 Seiten, Illustrationen, Diagramme
Publisher	Humana Press
Publishing place	New York, NY
Publishing country	United States
Document type	Book
HBZ-ID	HT019862553
ISBN	978-1-4939-8756-6 ; 9781493987573 ; 1-4939-8756-9 ; 1493987577
Database	Catalogue ZB MED Medicine, Health

In stock of ZB MED Cologne/Königswinter

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Zs A 7042 -1859-	verfügbar in Königswinter	Königswinter

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Article: Omics-Driven Biotechnology for Industrial Applications.

Amer, Bashar / Baidoo, Edward E K

Frontiers in bioengineering and biotechnology

2021 Volume 9, Page(s) 613307

Abstract: Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based ... ...

Abstract	Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.
Language	English
Publishing date	2021-02-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2021.613307
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Article ; Online: Microbial Metabolomics: A General Overview.

Baidoo, Edward E K

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1859, Page(s) 1–8

Abstract: In the biosciences, there has been growing interest in the elucidation of gene function. Consequently, metabolomics has garnered a lot of attention of late due to its provision of metabolic information pertaining to both function and phenotype. ... ...

Abstract	In the biosciences, there has been growing interest in the elucidation of gene function. Consequently, metabolomics has garnered a lot of attention of late due to its provision of metabolic information pertaining to both function and phenotype. Furthermore, when metabolomics data is integrated with other "omics" data, precise characterization of metabolic activity can be achieved. This chapter briefly introduces a few important aspects of the metabolome, the challenges faced when acquiring metabolomic information and the steps that are necessary to overcoming them. This chapter also briefly covers current analytical technologies and some microbial metabolomic applications.
MeSH term(s)	Bacteria/metabolism ; Fungi/metabolism ; Magnetic Resonance Spectroscopy/methods ; Mass Spectrometry/methods ; Metabolic Networks and Pathways/genetics ; Metabolome/physiology ; Metabolomics/methods
Language	English
Publishing date	2018-11-12
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8757-3_1
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Article ; Online: Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit.

Maini Rekdal, Vayu / van der Luijt, Casper R B / Chen, Yan / Kakumanu, Ramu / Baidoo, Edward E K / Petzold, Christopher J / Cruz-Morales, Pablo / Keasling, Jay D

Nature communications

2024 Volume 15, Issue 1, Page(s) 2099

Abstract: Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and ... ...

Abstract	Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.
MeSH term(s)	Synthetic Biology/methods ; Gene Editing ; Aspergillus oryzae/genetics ; Aspergillus oryzae/metabolism ; Mycelium/genetics ; Heme/metabolism
Chemical Substances	Heme (42VZT0U6YR)
Language	English
Publishing date	2024-03-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46314-8
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Article ; Online: Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications.

Baidoo, Edward E K / Teixeira Benites, Veronica

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1859, Page(s) 11–69

Abstract: The demand for understanding the roles genes play in biological systems has steered the biosciences into the direction the metabolome, as it closely reflects the metabolic activities within a cell. The importance of the metabolome is further highlighted ... ...

Abstract	The demand for understanding the roles genes play in biological systems has steered the biosciences into the direction the metabolome, as it closely reflects the metabolic activities within a cell. The importance of the metabolome is further highlighted by its ability to influence the genome, transcriptome, and proteome. Consequently, metabolomic information is being used to understand microbial metabolic networks. At the forefront of this work is mass spectrometry, the most popular metabolomics measurement technique. Mass spectrometry-based metabolomic analyses have made significant contributions to microbiological research in the environment and human disease. In this chapter, we break down the technical aspects of mass spectrometry-based metabolomics and discuss its application to microbiological research.
MeSH term(s)	Analytic Sample Preparation Methods/instrumentation ; Analytic Sample Preparation Methods/methods ; Archaea/metabolism ; Bacteria/metabolism ; Data Analysis ; Data Mining/methods ; Mass Spectrometry/instrumentation ; Mass Spectrometry/methods ; Metabolic Networks and Pathways/genetics ; Metabolome/physiology ; Metabolomics/instrumentation ; Metabolomics/methods ; Microbiota/physiology ; Yeasts/metabolism
Language	English
Publishing date	2018-11-12
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8757-3_2
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Article: Downregulation of Squalene Synthase Broadly Impacts Isoprenoid Biosynthesis in Guayule.

Placido, Dante / Dong, Niu / Amer, Bashar / Dong, Chen / Ponciano, Grisel / Kahlon, Talwinder / Whalen, Maureen / Baidoo, Edward E K / McMahan, Colleen

Metabolites

2022 Volume 12, Issue 4

Abstract: Production of natural rubber ... ...

Abstract	Production of natural rubber by
Language	English
Publishing date	2022-03-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo12040303
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Article ; Online: Distinct functional roles for hopanoid composition in the chemical tolerance of Zymomonas mobilis.

Brenac, Léa / Baidoo, Edward E K / Keasling, Jay D / Budin, Itay

Molecular microbiology

2019 Volume 112, Issue 5, Page(s) 1564–1575

Abstract: Hopanoids are a class of membrane lipids found in diverse bacterial lineages, but their physiological roles are not well understood. The ethanol fermenter Zymomonas mobilis features the highest measured concentration of hopanoids, leading to the ... ...

Abstract	Hopanoids are a class of membrane lipids found in diverse bacterial lineages, but their physiological roles are not well understood. The ethanol fermenter Zymomonas mobilis features the highest measured concentration of hopanoids, leading to the hypothesis that these lipids can protect against the solvent toxicity. However, the lack of genetic tools for manipulating hopanoid composition in this bacterium has limited their further functional analysis. Due to the polyploidy (>50 genome copies per cell) of Z. mobilis, we found that disruptions of essential hopanoid biosynthesis (hpn) genes act as genetic knockdowns, reliably modulating the abundance of different hopanoid species. Using a set of hpn transposon mutants, we demonstrate that both reduced hopanoid content and modified hopanoid polar head group composition mediate growth and survival in ethanol. In contrast, the amount of hopanoids, but not their head group composition, contributes to fitness at low pH. Spectroscopic analysis of bacterial-derived liposomes showed that hopanoids protect against several ethanol-driven phase transitions in membrane structure, including lipid interdigitation and bilayer dissolution. We propose that hopanoids act through a combination of hydrophobic and inter-lipid hydrogen bonding interactions to stabilize bacterial membranes during solvent stress.
MeSH term(s)	Anti-Infective Agents, Local/pharmacology ; Cell Membrane/metabolism ; Drug Tolerance/genetics ; Ethanol/pharmacology ; Membrane Lipids/classification ; Membrane Lipids/metabolism ; Solvents/pharmacology ; Stress, Physiological/drug effects ; Stress, Physiological/genetics ; Triterpenes/metabolism ; Zymomonas/drug effects ; Zymomonas/genetics
Chemical Substances	Anti-Infective Agents, Local ; Membrane Lipids ; Solvents ; Triterpenes ; Ethanol (3K9958V90M)
Language	English
Publishing date	2019-09-17
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.14380
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Article ; Online: Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria.

Chen, Xiaoyue / Hudson, Graham A / Mineo, Charlotte / Amer, Bashar / Baidoo, Edward E K / Crowe, Samantha A / Liu, Yuzhong / Keasling, Jay D / Scheller, Henrik V

Nature communications

2023 Volume 14, Issue 1, Page(s) 7101

Abstract: Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. Saponaria vaccaria is an annual herb used in traditional Chinese medicine, containing large quantities of oleanane-type triterpenoid saponins ... ...

Abstract	Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. Saponaria vaccaria is an annual herb used in traditional Chinese medicine, containing large quantities of oleanane-type triterpenoid saponins with anticancer properties and structural similarities to the vaccine adjuvant QS-21. Leveraging the MeJA-elicited saponin biosynthesis, we identify multiple enzymes catalyzing the oxidation and glycosylation of triterpenoids in S. vaccaria. This exploration is aided by Pacbio full-length transcriptome sequencing and gene expression analysis. A cellulose synthase-like enzyme can not only glucuronidate triterpenoid aglycones but also alter the product profile of a cytochrome P450 monooxygenase via preference for the aldehyde intermediate. Furthermore, the discovery of a UDP-glucose 4,6-dehydratase and a UDP-4-keto-6-deoxy-glucose reductase reveals the biosynthetic pathway for the rare nucleotide sugar UDP-D-fucose, a likely sugar donor for fucosylation of plant natural products. Our work enables the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.
MeSH term(s)	Triterpenes/metabolism ; Transcriptome ; Saponaria/genetics ; Saponaria/metabolism ; Vaccaria/genetics ; Plants/metabolism ; Saponins ; Uridine Diphosphate ; Glucose ; Sugars
Chemical Substances	Triterpenes ; methyl jasmonate (900N171A0F) ; Saponins ; Uridine Diphosphate (58-98-0) ; Glucose (IY9XDZ35W2) ; Sugars
Language	English
Publishing date	2023-11-04
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42877-0
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Article ; Online: Engineering Saccharomyces cerevisiae for isoprenol production.

Kim, Jinho / Baidoo, Edward E K / Amer, Bashar / Mukhopadhyay, Aindrila / Adams, Paul D / Simmons, Blake A / Lee, Taek Soon

Metabolic engineering

2021 Volume 64, Page(s) 154–166

Abstract: Isoprenol (3-methyl-3-butene-1-ol) is a valuable drop-in biofuel and an important precursor of several commodity chemicals. Synthetic microbial systems using the heterologous mevalonate pathway have recently been developed for the production of isoprenol ...

Abstract	Isoprenol (3-methyl-3-butene-1-ol) is a valuable drop-in biofuel and an important precursor of several commodity chemicals. Synthetic microbial systems using the heterologous mevalonate pathway have recently been developed for the production of isoprenol in Escherichia coli, and a significant yield and titer improvement has been achieved through a decade of research. Saccharomyces cerevisiae has been widely used in the biotechnology industry for isoprenoid production, but there has been no good example of isoprenol production reported in this host. In this study, we engineered the budding yeast S. cerevisiae for improved biosynthesis of isoprenol. The strain engineered with the mevalonate pathway achieved isoprenol production at the titer of 36.02 ± 0.92 mg/L in the flask. The IPP (isopentenyl diphosphate)-bypass pathway, which has shown more efficient isoprenol production by avoiding the accumulation of the toxic intermediate in E. coli, was also constructed in S. cerevisiae and improved the isoprenol titer by 2-fold. We further engineered the strains by deleting a promiscuous endogenous kinase that could divert the pathway flux away from the isoprenol production and improved the titer to 130.52 ± 8.01 mg/L. Finally, we identified a pathway bottleneck using metabolomics analysis and overexpressed a promiscuous alkaline phosphatase to relieve this bottleneck. The combined efforts resulted in the titer improvement to 383.1 ± 31.62 mg/L in the flask. This is the highest isoprenol titer up to date in S. cerevisiae and this work provides the key strategies to engineer yeast as an industrial platform for isoprenol production.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Metabolic Engineering ; Mevalonic Acid ; Saccharomyces cerevisiae/genetics
Chemical Substances	Escherichia coli Proteins ; Mevalonic Acid (S5UOB36OCZ)
Language	English
Publishing date	2021-02-10
Publishing country	Belgium
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2021.02.002
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Article ; Online: In-planta production of the biodegradable polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC): Stacking reduced biomass recalcitrance with value-added co-product.

Lin, Chien-Yuan / Vuu, Khanh M / Amer, Bashar / Shih, Patrick M / Baidoo, Edward E K / Scheller, Henrik V / Eudes, Aymerick

Metabolic engineering

2021 Volume 66, Page(s) 148–156

Abstract: 2-Pyrone-4,6-dicarboxylic acid (PDC), a chemically stable intermediate that naturally occurs during microbial degradation of lignin by bacteria, represents a promising building block for diverse biomaterials and polyesters such as biodegradable plastics. ...

Abstract	2-Pyrone-4,6-dicarboxylic acid (PDC), a chemically stable intermediate that naturally occurs during microbial degradation of lignin by bacteria, represents a promising building block for diverse biomaterials and polyesters such as biodegradable plastics. The lack of a chemical synthesis method has hindered large-scale utilization of PDC and metabolic engineering approaches for its biosynthesis have recently emerged. In this study, we demonstrate a strategy for the production of PDC via manipulation of the shikimate pathway using plants as green factories. In tobacco leaves, we first showed that transient expression of bacterial feedback-resistant 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (AroG) and 3-dehydroshikimate dehydratase (QsuB) produced high titers of protocatechuate (PCA), which was in turn efficiently converted into PDC upon co-expression of PCA 4,5-dioxygenase (PmdAB) and 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (PmdC) derived from Comamonas testosteroni. We validated that stable expression of AroG in Arabidopsis in a genetic background containing the QsuB gene enhanced PCA content in plant biomass, presumably via an increase of the carbon flux through the shikimate pathway. Further, introducing AroG and the PDC biosynthetic genes (PmdA, PmdB, and PmdC) into the Arabidopsis QsuB background, or introducing the five genes (AroG, QsuB, PmdA, PmdB, and PmdC) stacked on a single construct into wild-type plants, resulted in PDC titers of ~1% and ~3% dry weight in plant biomass, respectively. Consistent with previous studies of plants expressing QsuB, all PDC producing lines showed strong reduction in lignin content in stems. This low lignin trait was accompanied with improvements of biomass saccharification efficiency due to reduced cell wall recalcitrance to enzymatic degradation. Importantly, most transgenic lines showed no reduction in biomass yields. Therefore, we conclude that engineering plants with the proposed de-novo PDC pathway provides an avenue to enrich biomass with a value-added co-product while simultaneously improving biomass quality for the supply of fermentable sugars. Implementing this strategy into bioenergy crops has the potential to support existing microbial fermentation approaches that exploit lignocellulosic biomass feedstocks for PDC production.
MeSH term(s)	Arabidopsis/genetics ; Biomass ; Lignin ; Polyesters ; Pyrones
Chemical Substances	Polyesters ; Pyrones ; alpha-pyrone-4,6-dicarboxylic acid (72698-24-9) ; Lignin (9005-53-2)
Language	English
Publishing date	2021-04-22
Publishing country	Belgium
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2021.04.011
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