Birgitta Ebert

Birgitta Ebert
The University of Queensland | UQ · Australian Institute for Bioengineering and Nanotechnology

Dr.-Ing.

About

81
Publications
19,455
Reads
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1,128
Citations
Citations since 2016
67 Research Items
917 Citations
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2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
Introduction
Birgitta Ebert currently works at the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland.

Publications

Publications (81)
Article
Triterpenoids are a subgroup of terpenoids and have wide applications in the food, cosmetics, and pharmaceutical industries. The heterologous production of various triterpenoids in Saccharomyces cerevisiae, as well as other microbes, has been successfully implemented as these production hosts not only produce the precursor of triterpenoids 2,3-oxid...
Preprint
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Triterpenoids, one of the most diverse classes of natural products, have been used for centuries as active ingredients in essential oils and Chinese medicines and are of interest for many industrial applications ranging from low-calorie sweeteners to cosmetic ingredients and vaccine adjuvants. However, not only can the extraction from plant materia...
Article
Cyanobacteria are photosynthetic prokaryotes with strong potential to be used for industrial terpenoid production. However, the key enzymes forming the principal terpenoid building blocks, called short‐chain prenyltransferases (SPTs), are insufficiently characterized. Here, we examined SPTs in the model cyanobacteria Synechococcus elongatus sp. PCC...
Chapter
Isoprenoids, also known as terpenes or terpenoids, are compounds made of one or more isoprene (C5H8) moieties and constitute the largest class of natural products. They play diverse roles in biology and have broad industrial uses as flavors, fragrances, biofuels, polymers, agricultural chemicals, and medicines. Most isoprenoids are secondary plant...
Article
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The yeast Ogataea polymorpha is an upcoming host for bio-manufacturing due to its unique physiological properties, including its broad substrate spectrum, and particularly its ability to utilize methanol as the sole carbon and energy source. However, metabolic engineering tools for O. polymorpha are still rare. In this study we characterized the in...
Article
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The strigolactone (SL) class of phytohormones shows broad chemical diversity, the functional importance of which remains to be fully elucidated, along with the enzymes responsible for the diversification of the SL structure. Here we explore the functional evolution of the highly conserved CYP711A P450 family, members of which catalyse several key m...
Article
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The yeast Saccharomyces cerevisiae uses the pyruvate dehydrogenase‐bypass for acetyl‐CoA biosynthesis. This relatively inefficient pathway limits production potential for acetyl‐CoA‐derived biochemical due to carbon loss and the cost of two high‐energy phosphate bonds per molecule of acetyl‐CoA. Here, we attempted to improve acetyl‐CoA production e...
Article
Full-text available
Background Ogataea polymorpha is a thermotolerant, methylotrophic yeast with significant industrial applications. While previously mainly used for protein synthesis, it also holds promise for producing platform chemicals. O. polymorpha has the distinct advantage of using methanol as a substrate, which could be potentially derived from carbon captur...
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It is generally recognized that proteins constitute the key cellular component in shaping microbial phenotypes. Due to limited cellular resources and space, optimal allocation of proteins is crucial for microbes to facilitate maximum proliferation rates while allowing a flexible response to environmental changes. To account for the growth condition...
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In metabolic engineering, loss-of-function experiments are used to understand and optimise metabolism. A conditional gene inactivation tool is required when gene deletion is lethal or detrimental to growth. Here, we exploit auxin-inducible protein degradation as a metabolic engineering approach in yeast. We demonstrate its effectiveness using terpe...
Article
Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpreta...
Article
Methyl ketones present a group of highly reduced platform chemicals industrially produced from petroleum-derived hydrocarbons. They find applications in the fragrance, flavor, pharmacological, and agrochemical industries, and are further discussed as biodiesel blends. In recent years, intense research has been carried out to achieve sustainable pro...
Preprint
Full-text available
Methyl ketones present a group of highly reduced platform chemicals industrially produced from petroleum-derived hydrocarbons. They find applications in the fragrance, flavor, pharmacological, and agrochemical industries, and are further discussed as biodiesel blends. In recent years, intense research has been carried out to achieve sustainable pro...
Article
While Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and, consequently, competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
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Proteins have generally been recognized to constitute the key cellular component in shaping microbial phenotypes. Due to limited cellular resources and space, optimal allocation of proteins is crucial for microbes to facilitate maximum proliferation rates while allowing a flexible response to environmental changes. Regulatory patterns of protein al...
Article
Full-text available
High gene expression of enzymes partaking in recombinant production pathways is a desirable trait among cell factories belonging to all different kingdoms of life. High enzyme abundance is generally aimed for by utilizing strong promoters, which ramp up gene transcription and mRNA levels. Increased protein abundance can alternatively be achieved by...
Article
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Um eine Professur zu übernehmen, bedarf es einer Fülle an formalen Voraussetzungen und die Wege dorthin sind vielfältig und häufig verworren. Welcher dieser Wege ans Ziel führt, ist neben dem Alter und der Publikationsleistung auch stark von der Kultur der Wissenschaftsbereiche abhängig. Während in den Naturwissenschaften eine Habilitation oft noch...
Article
Full-text available
Exploring the dynamic behavior of cellular metabolism requires a standard laboratory method that guarantees rapid sampling and extraction of the cellular content. We propose a versatile sampling technique applicable to cells with different cell wall and cell membrane properties. The technique is based on irreversible electroporation with simultaneo...
Preprint
Full-text available
High gene expression of enzymes partaking in recombinant production pathways is a desirable trait among cell factories belonging to all different kingdoms of life. High enzyme abundance is generally aimed for by utilizing strong promoters, which ramp up gene transcription and mRNA levels. Increased protein abundance can alternatively be achieved by...
Article
Full-text available
Fatty alcohols are widely used in various applications within a diverse set of industries, such as the soap and detergent industry, the personal care, and cosmetics industry, as well as the food industry. The total world production of fatty alcohols is over 2 million tons with approximately equal parts derived from fossil oil and from plant oils or...
Article
Full-text available
Metabolic coupling of product synthesis and microbial growth is a prominent approach for maximizing production performance. Growth-coupling (GC) also helps stabilizing target production and allows the selection of superior production strains by adaptive laboratory evolution. To support the implementation of growth-coupling strain designs, we seek t...
Article
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Dicarboxylic acids are important biobased building blocks, and Saccharomyces cerevisiae is postulated to be an advantageous host for their fermentative production. Here, we engineered a pyruvate‐decarboxylase‐negative S. cerevisiae strain for succinic acid production to exploit its promising properties, i.e., lack of ethanol production and accumula...
Preprint
Exploring the dynamic behavior of cellular metabolism requires a standard laboratory method that guarantees rapid sampling and extraction of the cellular content. We propose a versatile sampling technique applicable to cells with different cell wall and cell membrane properties. The technique is based on irreversible electroporation with simultaneo...
Article
Full-text available
Background Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of t...
Preprint
Obligate aerobic organisms rely on a functional electron transport chain for energy generation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. We here investigated the esse...
Article
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An efficient route to obtain aromatic products based on biomass feedstock is a challenge for future biorefineries. Isobutyraldehyde is a promising feedstock available via biotechnological routes based on both carbohydrates and the direct bioconversion of CO 2 . Herein, we report an efficient process for the aromatisation of isobutyraldehyde over ze...
Article
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Saccharomyces cerevisiae is a yeast cell factory of choice for the production of many bio‐based chemicals. However, it is also a Crabtree‐positive yeast and so it shuttles a large portion of carbon into ethanol, even under aerobic conditions. To minimise the carbon loss, ethanol formation can be eliminated by deleting pyruvate decarboxylase (PDC) a...
Article
Die Zahl akademischer Nachwuchsführungskräfte ist in den vergangenen zehn Jahren stark gestiegen. Nicht immer geht mit einer Zunahme an Pflichten auch ein Mehr an Rechten einher. Nachwuchsführungskräfte des Zukunftsforums Biotechnologie der DECHEMA unterbreiten Verbesserungsvorschläge. Link zum Artikel. https://www.wissenschaftsmanagement-online.d...
Article
Full-text available
Heterologous synthesis of triterpenoids in Saccharomyces cerevisiae from its native metabolite squalene has been reported to offer an alternative to chemical synthesis and extraction from plant material if productivities can be increased. Here, we physiologically characterized a squalene overproducing S. cerevisiae CEN.PK strain to elucidate the ef...
Article
Full-text available
The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia towards sustainable production of the 2nd generation of biofuels, with Methyl Ethyl Ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent....
Data
Supplementary material. Supplementary file 2: Matlab scripts for reproducing the presented simulations.
Data
Supplementary material. Supplementary file 1: Extended version of Table 2.
Preprint
Full-text available
Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed. Here, we present memote ( https://github...
Preprint
Full-text available
The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia towards sustainable production of the 2 nd generation of biofuels, with Methyl Ethyl Ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent...
Article
Full-text available
Microbial carbon dioxide assimilation and conversion to chemical platform molecules has the potential to be developed as economic, sustainable processes. The carbon dioxide assimilation can proceed by a variety of natural pathways and recently even synthetic CO2 fixation routes have been designed. Early assessment of the performance of the differen...
Article
Full-text available
To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness fun...
Preprint
Full-text available
To date, several independent methods and algorithms exist exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives as well as fitness function...
Preprint
Metabolic coupling of product synthesis and microbial growth is a prominent approach for maximizing production performance. Growth-coupling (GC) also helps stabilizing target production and allows the selection of superior production strains by adaptive laboratory evolution. We have developed the computational tool gcOpt, which identifies knockout...
Chapter
Rational strain engineering requires solid testing of phenotypes including productivity and ideally contributes thereby directly to our understanding of the genotype–phenotype relationship. Actually, the test step of the strain engineering cycle becomes the limiting step, as ever advancing tools for generating genetic diversity exist. Here, we brie...
Article
Volatile organic compounds (VOCs) are small molecular mass substances, which exhibit low boiling points and high-vapour pressures. They are ubiquitous in nature and produced by almost any organism of all kingdoms of life. VOCs are involved in many inter- and intraspecies interactions ranging from antimicrobial or fungal effects to plant growth prom...
Article
Full-text available
While yeast is one of the most studied organisms, its intricate biology remains to be fully mapped and understood. This is especially the case when it comes to capture rapid, in vivo fluctuations of metabolite levels. Secondary electrospray ionization-high resolution mass spectrometry SESI-HRMS is introduced here as a sensitive and noninvasive anal...
Article
Microbial production of plant derived, biologically active compounds has the potential to provide economic and ecologic alternatives to existing low productive, plant-based processes. Current production of the pharmacologically active cyclic triterpenoid betulinic acid is realized by extraction from the bark of plane tree or birch. Here, we reengin...
Article
Full-text available
Recent advances in the availability and applicability of genetic tools for non-conventional yeasts have raised high hopes regarding the industrial applications of such yeasts; however, quantitative physiological data on these yeasts, including intracellular flux distributions, are scarce and have rarely aided in the development of novel yeast appli...
Article
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Background: Volatile organic compounds (VOCs) are small molecular mass substances, which exhibit high-vapor pressures, low boiling points, and lipophilic character. VOCs are produced by all organisms including eukaryotic microbes like yeast, which volatile metabolites are for centuries exploited for examples as flavors in bread, beer, and wine. Not...
Article
Pseudomonas putida efficiently utilizes many different carbon sources without the formation of byproducts even under conditions of stress. This implies a high degree of flexibility to cope with conditions that require a significantly altered distribution of carbon to either biomass or energy in the form of NADH. In literature, co-feeding of the red...
Article
Full-text available
Background In the future, oil- and gas-derived polymers may be replaced with bio-based polymers, produced from renewable feedstocks using engineered cell factories. Acrylic acid and acrylic esters with an estimated world annual production of approximately 6 million tons by 2017 can be derived from 3-hydroxypropionic acid (3HP), which can be produce...