Research
Current Projects
Completed Projects (Selection)
Additional Completed Projects (Selection)
- HotSysAPP (BMBF, 031L0078A)
- SulfoSYSBIOTEC (BMBF, 0316188A)
- HotZyme (EU, 265933)
- ExpresSYS (BMBF, 0315586C)
- SulfoSYS (BMBF, 0315004A)
Lipid║Divide - Resolving the ‘lipid divide’ by unravelling the evolution and role of fatty acid metabolic pathways in Archaea
Prof. Dr. Bettina Siebers, Dr. Christopher Bräsen, Dr. Christian Schmerling, Dr. Christina Stracke
2019 Volkswagen Stiftung "Life?" A fresh scientific Approach to the Basic Principles of life
Joint Proposal by (from left to right) Dr. Sven Meckelmann (Applied Analytical Chemistry, Chemistry, UDE), Prof. Bettina Siebers (MEB, UMB, UDE), Dr. Christopher Bräsen (MEB, UMB, UDE), Prof. Dr. Markus Kaiser (Chemical Biology, Biology, UDE), Prof. Dr. Thijs Ettema (Laboratory of Microbiology, Wageningen University, NL)
Summary. In biology, all known life forms have so far been assigned to one of the three domains: Bacteria, Archaea, or Eukarya. However, recent findings suggest that eukaryotes, including humans, originated from the domain Archaea. This has led to a revised "two-domain model" of the universal phylogenetic tree of life. This two-domain model raises a fundamental biological question: a defining characteristic of all known life forms is that they are composed of cells as basic units, and these cells are separated from their environment by lipid membranes. The membranes of Archaea are composed of lipids with isoprenoid side chains that are linked to glycerol-1-phosphate (G1P) via ether bonds. This composition is fundamentally different from the lipids of Bacteria and Eukarya, which consist of fatty acid side chains linked to glycerol-3-phosphate (G3P) via ester bonds. Thus, during the evolution of eukaryotes from archaeal ancestors, a fundamental shift in membrane lipid composition must have occurred. How and why this so-called "lipid divide" took place remains one of the unresolved fundamental questions in evolutionary biology. This proposed project aims to address this question by investigating the fatty acid metabolism and functions of fatty acids in Archaea and correlating these findings with sequence comparisons of genes and genomes (phylogenomics). This project will thus contribute to a deeper understanding of eukaryotic evolution and, by extension, the origin of life in general.
ARCTECH - Harnessing the potential of Archaea – Training Europe’s next visionaries for an innovative and sustainable future
European Commission, Horizon MSCA 101120407
Prof. Dr. Bettina Siebers, Dr. Laura Kuschmierz, M.Sc. Sergio Scotillo
Project partners. Prof. Dr. Tessa Quax (University of Groningen), Prof. Dr. Christine Moissl-Eichinger (Medical University of Graz), Prof. Dr. Sonja-Verena Albers (University of Freiburg), Prof. Dr. Marco Moracci (University of Naples Federico II), Linda Dengler (Microbify), Dr. Pierre Türschmann (Interherence), Dr. Hanna Oksanen (University of Helsinki)
Associated partners. Prof. Dr. Martin Pilhofer (ETH Zürich), Dr. Kenneth Jensen (Novonesis) and Prof. Dr. Bertram Daum (University of Exeter).
ARCTECH project homepage Linked-in Instagram Bluesky YouTube
Summary. Archaea, with their remarkable adaptability to extreme environments such as high pressures, salt concentrations, and temperatures, hold immense promise for biotechnological applications. Despite their extraordinary biochemical and metabolic properties, our limited understanding of the structure and function of archaeal cell surfaces, also in the context of biofilm formation, has hindered their industrial use. In the framework of Horizon Europe’s Marie Skłodowska-Curie Actions, funded by the European Commission, ARCTECH seeks to bridge critical knowledge gaps and develop methodologies necessary to unleash the biotechnological potential of Archaea. ARCTECH proposes the first training initiative on Archaea, aiming to foster the next generation of European visionaries in fundamental archaeal research and their application in biotechnology.
Exploring Biofilm Formation and Extracellular Polymeric Substances (EPS). Within the framework of ARCTECH, our primary objective is to dissect the essential steps involved in archaeal biofilm formation and devise strategies to intervene in this process. This entails a comprehensive analysis of biofilm formation and dispersion, coupled with an investigation into the quantity and composition of their extracellular polymeric substances (EPS), encompassing exopolysaccharides, DNA, and proteins. In particular, the structure of the exopolysaccharide produced by Sulfolobus acidocaldarius is being determined in collaboration with ARCTECH partners.
Unraveling Enzymes for Biotechnological Applications. Within ARCTECH, we explore enzymes implicated in EPS degradation, such as proteases and glycoside hydrolases involved in the process of biofilm dispersion. The identification of these proteins is accomplished by bioinformatic prediction, activity-based protein profiling and proteomics. Through expression, purification, and characterization, we aim to identify novel enzymes with potential biotechnological applications. Their resilience in the context of industrially relevant conditions will be evaluated to assess their suitability for biotechnological processes.
Funded by the European Union under Grant Agreement n. 101120407. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them.
GlycoN - GLYCO protein N-glycosylation from non-life to eukaryotes - a Doctoral Network to expand the knowledge on a ubiquitous post translational modification of proteins
Europäische Kommission, Grant Agreement 101119499
Prof. Dr. Bettina Siebers, Dr. Laura Kuschmierz, M.Sc. Alberto Bobbio
Project partners. Prof. Dr. Antonio Molinaro (University of Naples Federico II), Prof. Dr. Hermen Overkleeft (Leiden University), Prof. Dr. Jesùs Jiménez Barbero (Center for Cooperative Research in Biosciences), Prof. Dr. Carme Rovira (University of Barcelona), Prof. Dr. Bernard Henrissat (Technical University of Denmark), Prof. Dr. Muriel Bardor (University of Rouen Normandy). GlycoN project homepage
Summary. The training network GLYCO-N, funded by the European Union, aims at training Doctoral Candidates to acquire the skills to develop different innovative strategies to
1) understand the diversity and structural complexity of archaeal, microalgal and viral N-glycosylation and
2) harness this knowledge for new solutions in biomedicine and biotechnology.
Protein N-glycosylation, the attachment of oligo- and polysaccharides at specific asparagine residues, is conserved throughout life, and even in the viral world. In contrast to eukaryotes, whose well-studied N-glycosylation machineries are relatively simple, archaea, microalgae, bacteria and some recently discovered viruses utilize a wide variety of monosaccharides to create a wealth of structurally diverse N-glycans. Because protein glycosylation occurs far downstream of protein synthesis the complexity and diversity in N-glycan structures are poorly understood in detail. This holds true specifically for N-glycosylation events that are the subject of the GLYCO-N program: those in archaea, microalgae and viruses. Understanding of the how and why of N-glycosylation in archaea, microalgae and viruses will open up many possibilities ranging from drug discovery (antivirals) to biotechnology (glycoprotein and glycoprocessing enzyme engineering for materials and life sciences).
Within GLYCO-N, we aim to study the function of glycosyltransferases in the thermophilic, archaeal model organism Sulfolobus acidocaldarius to unravel their potential for biotechnological application. While 29 genes are annotated to encode glycosyltransferases (GTs), their possible involvement in N-glycosylation for example in response to changing conditions such as available carbon sources or stresses, and detailed enzymatic studies are still missing for most GTs, hampering their use in biotechnological applications. Further, the functional characterization of GTs and the analysis of the N-glycan pathway in S. acidocaldarius will provide essential information for phylogenetic analysis to retrieve evolutionary implications. Our study combines the analysis of glucan composition and structure, using available GT mutants, with multiomics studies and the enzymatic characterization of GTs in close collaboration with GLYCO-N partners.
Funded by the European Union under Grant Agreement n. 101119499. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them.
SCyCode - Unraveling the cyanobacterial carbon switch and its regulation using enzyme kinetic analyses and mathematical modelling
DFG, Joint Research Project (Research group). SCyCode - The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers;
Prof. Dr. Bettina Siebers, M.Sc. Carmen Peraglie, M.Sc. Ravi Ojha
Project coordination: Prof. Dr. Karl Forchhammer (University of Tübingen). SCyCode FOR2816 project homepage
Summary. Cyanobacteria, such as Synechocystis sp. PCC 6803, are capable of switching between photoautotrophic and heterotrophic metabolism. Previous studies have shown that, in addition to the day/night cycle, the availability of inorganic carbon and changes in nitrogen supply can also trigger this switching process. The glycogen metabolism and the conversion of triose phosphates have been identified as potential central control points. Interestingly, the primary metabolism of Synechocystis is characterized by parallel metabolic pathways and numerous isoenzymes. We hypothesize that these isoenzymes possess distinct kinetic and regulatory properties, enabling them to function as control points between autotrophic and heterotrophic metabolism. As part of the overarching goal of the SCyCode research group—to unravel the different regulatory layers underlying the switch between autotrophic and heterotrophic metabolism—this subproject aims to identify the corresponding metabolic control points by combining detailed enzyme characterizations with mathematical modeling (in collaboration with co-partner Jacky Snoep, University of Stellenbosch, South Africa).
MetaboArchaea - D-Mannose and D-fructose utilization in members of the Sulfolobales – Significance of the upper Embden-Meyerhof-Parnas pathway
DFG, Prof. Dr. Bettina Siebers, M.Sc. Anna Ebel, PD Dr. Meina Neumann-Schaal, M.Sc. Kea Mucha (Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig)
Summary. Carbohydrate metabolism in archaeal organisms plays a crucial role in their survival and adaptation to varying environmental conditions. Understanding the pathways involved in the utilization of specific sugars such as D-mannose and D-fructose is essential for unraveling the metabolic intricacies of these organisms. Within the DFG-funded project MetaboArchaea we aim to decipher the pathways for D-mannose and D-fructose degradation in Sacch. solfataricus and study the formation and utilization of D-mannose in S. acidocaldarius in collaboration with Meina Neumann-Schaal (DSMZ Braunschweig).
Identification of D-mannose and D-fructose degradation pathways in Saccharolobus solfataricus. In particular, comparative transcriptomics, proteomics, metabolomics, and crude extract measurements will be performed to identify the respective degradation pathways. The fate of carbon derived from D-mannose and D-fructose will be studied in Saccharolobus solfataricus using high-resolution 13C-based mass spectrometry to unravel the respective metabolic fluxes.
D-Mannose and NDP-mannose formation in S. acidocaldarius and its role in cellular processes. The synthesis of phosphorylated and activated D-mannose derivatives in S. acidocaldarius will be studied to address their role in cellular processes such as protein N-glycosylation and as a component of exopolysaccharides in extracellular polymeric substances. Deletion strains will be constructed and analysed concerning their phenotypes. Enzymes involved in carbohydrate metabolism are heterologously and/or homologously expressed, purified, and enzymatically characterized to unravel their kinetic and regulatory properties. Altogether, we aim to provide crucial insights into the complexity and regulation of carbohydrate metabolism in both archaeal model organisms.
HotPETresolve - Activity-Based Protein Profiling for the Identification of New Thermostable Polyethylene Terephthalate (PET) Degrading Enzymes for Biorecycling
Bioökonomie International 2022, Prof. Dr. Bettina Siebers, Dr. Christian Schmerling, Prof. Dr. Markus Kaiser, M.Sc. Leonard Sewald (University of Duisburg-Essen).
Associated partners. Dr. Kenneth Jensen (Novonesis, Denmark) and Prof. Dr. Eric Boyd (Montana State University, USA)
Summary. Plastics such as PET are globally used materials. Unfortunately, their extensive use has led to an undesirable accumulation in the environment. It is estimated that 150–200 million tons of plastic have already accumulated in landfills or the natural environment, with this figure continuing to rise. The weathering of these plastics results in the formation of smaller micro- and nanoplastic particles, whose effects on human and animal health remain unclear to this day. To address this global problem, the HotPETresolve project, in collaboration with Prof. Markus Kaiser (University of Duisburg-Essen), aims to identify new organisms and enzymes capable of enabling the biological degradation of PET on an industrial scale. While PET-degrading enzymes are already known, they lack long-term stability at the necessary process temperatures and sufficient enzymatic efficiency. Therefore, the discovery of enzymes with improved properties is a prerequisite for developing a market for PET enzyme-based degradation. In this project, funded by Bioeconomy International 2022, PET-degrading strains and biocatalysts will be identified through bioprospecting of thermophilic organisms, leveraging the natural diversity of such environments. Their discovery will rely on a novel approach combining environmental sampling and enrichment techniques with (meta-)genomics and activity-based protein profiling (ABPP). ABPP utilizes activity-based probes (ABPs) to specifically identify active enzymes. This approach enables the identification of enzymes directly from enrichment cultures and environmental samples, referred to as “environmental ABPP” (eABPP).
Completed projects (selected)
HotAcidFACTORY - Sulfolobus acidocaldarius as a Novel Thermoacidophilic Biofactory
BMBF Funding: "Microbial Biofactories for the Industrial Bioeconomy - Novel Platform Organisms for Innovative Products and Sustainable Bioprocesses"
Six (inter)national partners: Prof. Dr. Markus Kaiser (Chemical Biology, Biology, UDE), Prof. Dr. Oliver Schmitz (Applied Analytical Chemistry, Chemistry UDE), Prof. Dr. Sonja-Verena Albers (Molecular Biology of Archaea, University Freiburg), Prof. Dr. Jörn Kalinowski (CeBiTec, University of Bielefeld), Dr. Oliver Spadiut (Vienna University of Technology).
Summary. Archaea were first described as a distinct third domain of life about 40 years ago and are often the dominant group of organisms in extreme habitats. These archaeal representatives are characterized by their remarkable "robustness" and are referred to as extremophiles, with their enzymes known as extremozymes. Archaea generally possess unique cellular and metabolic properties, such as novel metabolic pathways or enzymes. The HotAcidFACTORY project aims to develop a practical and highly flexible bioproduction system (biofactory) based on the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius (Saci) (75–80 °C, pH 2–3), suitable for use in industrial processes under harsh reaction conditions. This novel bioproduction system is intended to enable the efficient production of extremozymes as well as other high-value products from industrial waste and by-products. Within the framework of the HotAcidFACTORY project, the following objectives will be pursued: (i) develop an improved genetic system for Saci to establish the organism as a novel platform for the expression of extremozymes and metabolic engineering; (ii) establish the utilization of alternative substrates, particularly industrial by-products and waste materials such as glycerol and CO2, by Saci; and (iii) optimize cultivation conditions for Saci, particularly for growth on glycerol and CO2, to achieve high cell densities suitable for industrial production and application processes.
ABPP_FUNGI – Activity-Based Protein Profiling (ABPP) for the Identification of New Hydrolases in Fungi
Mercur, Joint proposal with Prof. Dr. M. Kaiser (Chemical Biology, Biology, UDE; Coordinator), Prof. Dr. D. Begerow (Geobotany, RUB, Bochum)
Summary. Many applications of biotechnology focus on the identification of structurally novel enzymes with unique catalytic properties, for example, through systematic screening of various microorganisms. However, this process is very labor-intensive and is intended to be optimized in this project by using an alternative workflow based on the method of Activity-Based Protein Profiling (ABPP). This approach builds on previous work (Kaiser, Siebers, Nature Communications 2017, 8:15352), where we demonstrated the potential of ABPP to detect even the smallest amounts of enzymes in an in vivo approach, even under extreme culture conditions, thus establishing a method for identifying new enzymes directly in organisms. In the present project, this approach will be applied to thermophilic fungi, as they are among the most potent degraders of plant biomass and thus possess a unique repertoire of enzymes, which, however, has not yet been extensively explored for biotechnological applications, especially for the "degradation" of non-food biomass. Therefore, our project represents a combination of chemical biology, biotechnology, and biodiversity research.
Explo-Carb – Research on Carbohydrate Metabolism in Hyperthermophilic Archaea: New Approaches, Enzymes, and Metabolic Pathways
DFG-RSF Cooperation: Joint German-Russian project proposals in life sciences, social sciences and humanities.
Prof. Dr. Bettina Siebers, Prof. Dr. Markus Kaiser (UDE), and Dr. Ilya V. Kublanov (Ferderal Research Center of Biotechnology RAS, Moscow)
Summary. Archaea possess unusual metabolic pathways and enzymes. From a biological and particularly biotechnological perspective, (hyper)thermophilic archaea are of special interest, as they are optimally adapted to extreme environmental conditions (high temperatures, pH, etc.), and their enzyme repertoire thus represents an exciting source for the discovery of new biotechnologically useful enzymes (which are often referred to as "extremozymes"). However, broader applications of these archaeal enzymes and a deeper understanding of the unique metabolism of these archaea have so far been difficult due to insufficient methods for the systematic study of these organisms. In the Explo-Carb project, we aim to develop and apply new methodological approaches to explore these organisms. We will focus on glycoside hydrolases and the carbohydrate-degrading metabolism. To this end, we will establish activity-based protein profiling (ABPP) as a new approach to study these enzymes and the carbohydrate metabolism in selected (hyper)thermophilic archaea, in order to characterize the corresponding metabolic processes. Furthermore, new (hyper)thermophilic strains will be isolated using in situ enrichment techniques and characterized with our methodological repertoire, including ABPP. Additionally, the direct applicability of ABPP for chemical profiling of environmental enrichment cultures will be evaluated.
ArchaeaEPS - Archaeal Biofilms: Composition of Extracellular Polymeric Substances, Exopolysaccharide Synthesis and Transport in Sulfolobus acidocaldarius
Coordination by Prof. Dr. Bettina Siebers
DFG Joint proposal (UDE), Dr. Jost Wingender (EMB), Prof. Dr. Oliver Schmitz (Applied Analytical Chemistry)
Summary. Biofilms represent the most common life form for the vast majority of microorganisms on Earth. Biofilms formed by bacteria and eukaryotic microorganisms (fungi, algae), along with their extracellular polymeric substances (EPS), have been extensively studied. Representatives of the Archaea, as the third domain of life, have received special attention due to their adaptation to extreme environments. However, relatively little information exists about archaeal biofilms. In this project, Sulfolobus acidocaldarius, a thermophilic, aerobic representative of the Crenarchaeota, will be used to investigate biofilm formation and architecture, the composition of EPS, and the biosynthesis and transport of exopolysaccharides (PS), one of the main components of EPS. S. acidocaldarius is an ideal model organism due to its demonstrated biofilm formation ability, ease of cultivation under laboratory conditions, and genetic accessibility. A gene cluster containing 11 glycosyltransferases and 8 membrane proteins has been identified in the S. acidocaldarius genome, and preliminary experiments with two deletion mutants confirmed the predicted function of these proteins in PS biosynthesis and transport. The goal of the project is to combine current techniques for biofilm characterization and EPS analysis with a molecular genetic-biochemical approach to elucidate the synthesis and transport of PS, as well as changes in EPS composition in response to environmental conditions. This project will provide new insights into biofilm formation and composition in Archaea, as well as into extremozymes (GTs) of biotechnological interest.
HotSolute - Thermophilic bacterial and archaeal chassis for extremolyte production
BMBF/EU. ERA CoBioTech (Horizon 2020, Joint project)
Partners: Prof. Dr. Jennifer Littlechild (University of Exeter, UK), Dr. Daniela Moni (ICRM, CNR, Milan, Italy), Dr. Felix Müller (Evonik Industries AG, Essen, DE), Prof. Dr. Elizaveta Bonch-Osmolovskaya (Winogradsky Institute of Microbiology, Russian Academy of Sciences, Russia), Prof. Jacky Snoep (Stellenbosch University, Stellenbosch, South Africa)
Summary. The HotSolute project aims to produce "extremolytes" using thermophilic in vitro enzyme cascades and in vivo through novel thermophilic platform organisms, the bacterium Thermus thermophilus (Tth, 65-75°C, pH 7.0) and the thermoacidophilic archaeon Sulfolobus acidocaldarius (Saci, 75-80°C, pH 2-4). Extremolytes are low-molecular-weight compatible solutes that are accumulated intracellularly by thermophilic organisms in response to various stress factors, stabilizing cellular components such as proteins and membranes. With these properties, extremolytes hold outstanding potential for industrial applications, particularly in the food, medical/health protection, personal care, and cosmetics sectors. However, these extremolytes have not been efficiently produced in mesophilic host organisms, such as yeasts or E. coli, due to the thermophilic nature of the synthesis pathways/enzymes. The newly developed enzyme cascades and "whole-cell biocatalysts" will be used in the project for the production of the three extremolytes: cyclic 2,3-diphosphoglycerate (cDPG), di-myo-1,1’-inositol-phosphate (DIP), and mannosylglycerate (MG), which occur exclusively in hyperthermophilic organisms (with few exceptions for MG), but have not been synthesized in mesophilic host organisms so far.