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  • 24/5/22 The Endesfelder lab is looking for a new PhD/PostDoc, details here
  • Symposium 50 years IfMB June 9th '22
  • Antrittsvorlesung
    Prof. Ulrike Endesfelder
    Dies Academicus 18.05.2022,
    11.15 Uhr Hörsaal III, Hauptgebäude

 
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Research Interests

What we work on

Mechanisms of energy conservation in methanogenic archaea

Methanosarcina sp.

Methanogenic organisms belong to the kingdom of Archaea and are widespread in anoxic environments. The process of methanogenesis is important for the global carbon cycle because it represents the terminal step in the anaerobic breakdown of organic matter. Large amounts of methane escape into the atmosphere and act as greenhouse gas but are also used as renewable energy source in biogas facilities.

While we have focused on methanogens that thrive on acetate as substrate in recent years, we now focus on methanogenic archaea that are associated with the human microbiome. A representative of these human-associated organisms is Methanomassiliicoccus luminyensis, a member of the recently described order of Methanomassiliicoccales. M. luminyensis uses methylamines or methanol as substrates with H2 serving as reductant. Long doubling times along with low optical densities are characteristic for this species and reflect that M. luminyensis has adapted to substrates with very little nutritional value. Due to the enzyme set Methanomassiliicoccales are distinct from the classical methanogenic groups because they show characteristics of all methanogenic groups and are therefore regarded as hybrids of classical methanogens. The respiratory chain of the Methanomassiliicoccales is reduced to only a few enzyme complexes, e. g. compared to Methanosarcina mazei, and mirror a very specialized lifestyle with elaborate mechanisms to conserve energy. We mainly focus on enzymes and enzyme complexes that are involved in the energy metabolism in M. luminyensis with special focus on the F420 dehydrogenase and heterodisulfide reductases. Additionally, the growth behavior of the organism is part of our research interests to gain insights of how the organism persists and grows in the human intestines, a habitat that is characterized by high interspecific competition and favors organisms with fast growth rates and high cell yields. Many techniques are involved in this research, ranging from proton translocation measurements to anaerobic protein purification. Also the whole range of molecular biological techniques is involved to give us a comprehensive understanding of how these organisms thrive.

 

Exploring the oxidative potential of Gluconobacter oxydans

Gluconobacter oxydans

Gluconobacter oxydans catalyses the incomplete and regioselective oxidation of a wide range of carbohydrates and alcohols in a process that is referred to as oxidative fermentation. Because of this feature Gluconobacter strains are used for the production of several compounds of great industrial importance (e.g. L-sorbose for vitamin C synthesis and 1-amino-D-sorbitol for the production of the antidiabetic drug Miglitol).

To elucidate the overall metabolism, we overproduce, purify and characterize many G. oxydans enzymes in our lab. Many proteins have been produced in E. coli but there is an elevated need to produce proteins homologously in G. oxydans, so we have developed overexpression systems for this organism. In the focus of attention is the heterologous and homolous production of membrane proteins with unique cofactors such as PQQ. Methods involved in this project include homologous and heterologous protein production in G. oxydans and other bacteria, membrane protein purification, enzyme activity measurements, HPLC and NMR. Also many molecular biological techniques are routinely used in all projects involved.

 

Production of prebiotics and low-calorie sweeteners

Prebiotic foods support the growth of bacteria in the intestine which have a positive effect on human health. Hence, the focus of this project is the microbial production of prebiotic fructooligosaccharides (FOS) from the polyfructoses levan and inulin. A second aim of the project is the production of natural low-calorie sugar derivatives (LCSD). The basis for the microbiological production of these substances are bacteria from the non-pathogenic genus Gluconobacter, which have been used for decades for the production of foodstuffs (e.g. fruit juices) and food supplements (e.g. vitamin C).
Genes coding for the enzymes involved in product formation of FOS and LCSD are introduced into Gluconobacter species and the product yield is analyzed and optimized. The newly generated bacterial strains are used by industry partners for microbial biotransformation and the associated commercial production of fructooligosaccharides and low-calorie sweeteners.
First studies confirmed that enzymes can be produced in Gluconobacter oxydans which open the door to develop efficient methods for the production of low-calorie sweeteners. However, the production strain and the fermentation process need to be optimized. This approach includes the increase of enzyme production and turnover rates. Furthermore, we found that levan production of a Gluconobacter strain was higher than that of other well-studied levan producers. This strain will be used for the production of levan which will be enzymatically cleaved to form fructooligosaccharides. A similar strategy will be employed for the formation of fructooligosaccharides from inulin. Substrate consumption and product formation of genetically modified Gluconobacter strains will be analyzed and strategies will be developed to increase the product yields.

 

Physiology and biochemistry of the major players of the human gut microbiome

The human gut microbiota has been proposed as a crucial environmental factor that plays a major role in host physiology by affecting several processes ranging from maturation of the immune system, regulation of host metabolism and nutritional effects to transformation of bioactive compounds and many more. Increasing evidence indicates the impact of changes in the composition of the human gut bacteria on host metabolism and a variety of diseases. Compositional and functional alterations of the human gut microbial communities have been linked to malnutrition, obesity and obesity-related diseases such as cirrhosis and cardiovascular diseases. Moreover, alterations of the gut microbiome are connected to inflammatory bowel disease, colorectal cancer, neurodevelopmental disorders, and aging.

Genomic and metagenomic analysis have revealed an extensive metabolic repertoire encoded in the gut microbiome. However, measurement of the function and metabolic activity of the intestinal bacteria has not kept pace with the growing knowledge of microbial diversity. Increasing the knowledge of the link between microbial phylogeny and metabolic functionality and activity is vital to fully understand the role of the intestinal microbiota in human health and disease. To estimate and judge the influence and importance of bacteria in the human gut a comprehensive understanding of their physiology and metabolism, especially their mode of energy conservation, is necessary. Genomics, proteomics and other Omics as well as mathematical and computer-based models produce a wealth of qualitative in vitro data. However, without the knowledge of biological functions these approaches do not really improve our understanding of biochemical pathways and the physiology of microbial gut organisms. The computer-based reconstruction of metabolic pathways and biological functions of gene sequences can undoubtedly successful if well-established biochemical processes are considered. The situation is different if the pathways do not follow the main chemoorganotrophic metabolism or are specific for certain bacteria. Especially gut microorganisms possess special enzymes and metabolic pathways that are poorly represented in general databases. In this situation it is not sufficient to examine gut microbial profiles or to deduce metabolic pathways using automatically generated gene annotations from DNA sequencing projects. Rather it is necessary to combine bioinformatic predictions and biochemical realities, which is the main goal of our approach to characterize the human gut microbiome. Currently members of the genera Prevotella, Bacteroides and Akkermansia are in the focus of our research project all of which are of major importance for a functional and healthy intestinal tract.

 

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