Our research in bacterial physiology is mainly concerned with stress-adaptation responses in Gram-positive bacteria, in particular the model organism Bacillus subtilis and the pathogenic bacterium Staphylococcus aureus. Microorganisms must adapt to various adverse environmental conditions in their natural habitats, such as oxidative stress, heat or cold stress, osmotic stress, nutrient limitation, anaerobic conditions and exposure to antibiotics. To survive these conditions, bacteria have developed appropriate adaptive strategies using both specific and general stress responses. One of the best characterised stress responses in bacteria is the general stress response of B. subtilis controlled by the alternative sigma factor SigB.

In addition to gene-specific approaches, methods for genome-wide analysis of the proteome and the transcriptome are used, which enable a comprehensive characterisation of bacterial adaptation responses. For example, together with European partners, we have analysed the transcriptome of B. subtilis under more than 100 different growth and stress conditions in a large-scale study, thus creating a comprehensive transcriptome map and recording the expression profiles of all genes. Such approaches contribute to the elucidation of the complex regulatory processes that play a role in bacterial adaptation to changing environmental conditions. Thus, they ultimately serve the goal of better understanding the interactions between cellular components as well as the function of all proteins and functional RNAs of an organism.

Principal Investigators

Prof. Dr. Uwe Völker

Dr. Ulrike Mäder

Dr. Leif Steil

Dr. Alexander Reder

Research Assistants

Dr. Stephan Michalik

PhD students

Marco Harms

Maximilian Schedlowski

David Núnez Nepomuceno

Alexander Ganske

Technical Assistance

Marc Schaffer

Specific research projects

SECRETERS

SECRETERS - A new generation of microbial expression hosts and tools for the production of biotherapeutics and high-value enzymes (Horizon 2020 EU-funded project)

The SECRETERS European research training network aims to develop powerful new microbial platforms for the production of secreted high-quality recombinant proteins, with a special emphasis on therapeutic proteins (biotherapeutics) and industrial enzymes that are difficult to express. Both are important products for the EU biotechnology sector, with combined markets of over $140 billion per year. However, many proteins in these categories, especially disulphide-bonded proteins, pose severe problems in production.

SECRETERS involves a team of 15 PhD students and a close collaboration between five academic institutions with expertise in redox chemistry, synthetic biology and protein expression, and five non-academic partners including some of the leading biotherapeutic and industrial enzyme companies. The emphasis of the SECRETERS project is on three microbial production hosts: Escherichia coli, Bacillus subtilis and the yeast Pichia pastoris.

In our subproject, we investigate the responses of B. subtilis to oxidative and secretion stress during recombinant protein production by transcriptomics and proteomics approaches as well as the use of reporter plasmids. An in-depth knowledge of bacterial stress management and the underlying regulation networks will provide leads for the improvement of industrial Bacillus strains.

The general stress response of Bacillus subtilis

The regulon controlled by the alternative sigma factor SigB of B. subtilis comprises more than 200 genes, and activation of SigB leads to massive changes in the gene expression pattern of B. subtilis. Although the general stress response of B. subtilis is already very well characterised, there are several aspects that are not yet fully understood and are the subject of our research in this area. These include, in particular, the regulatory mechanisms responsible for specific expression patterns of subsets of the SigB regulon and the functional elucidation of SigB-regulated genes. An important focus of our work is also the integration of the SigB-dependent response into the regulatory network of non-growing cells.

Adaptation of Bacillus subtilis to changes in osmolarity

B. subtilis is found especially in the upper soil layers, where it is exposed to constant changes in the osmolarity of its environment. Due to desiccation of the soil on the one hand and heavy rainfall on the other, the osmotic conditions in the soil can fluctuate very strongly. To counteract dehydration and plasmolysis of the cells when external osmolarity increases, B. subtilis uses osmo-protective substances, so-called compatible solutes, such as proline and glycine betaine. These are accumulated intracellularly in high concentrations, enabling the cells to retain water and maintain turgor. In close cooperation with the research group of Prof. Erhard Bremer (Marburg), we analyse the regulation of synthesis and uptake systems for osmoprotective substances as well as the global changes in gene expression and physiology of B. subtilis under hyperosmotic conditions.

The role of global regulators and the transcription termination factor Rho in Staphylococcus aureus

We are investigating the adaptation to stress and nutrient conditions to which S. aureus is exposed in its interaction with the host, mainly using in vivo proteomic analyses (topic Host-pathogen interactions). A major goal of comparative analyses of wild-type S. aureus with strains carrying mutations in key regulators is to gain a deeper understanding of the regulatory networks that control the adaptation of bacterial physiology to the host environment and the synthesis of virulence factors. The alternative sigma factor SigB is a central regulator that also controls a large regulon in S. aureus, whose genes encode proteins that are involved in stress responses, cell wall and metabolic functions, among other things, but are also virulence factors. Our research group is particularly concerned with the importance of SigB for the survival of S. aureus in eukaryotic cells.

Another focus is the characterisation of the physiological role of the transcription termination factor Rho. As in other bacteria, an essential function of Rho in S. aureus is the repression of antisense transcription. Of particular interest, however, is that in S. aureus there is a pathophysiologically relevant link between the activity of Rho and the regulation of virulence factor genes, the molecular basis of which is being investigated in current work. In addition, we are characterising non-coding RNAs, which are also essential components of regulatory networks.