Projects

Protein homeostasis and stress response

We are interested in investigating the control of protein homeostasis in the Gram-positive model organism Bacillus subtilis, especially when exposed to stress conditions such as heat or oxidative stress. Most of the highly conserved chaperone and proteases of the cellular protein quality control network such as the Hsp70 and Hsp60 chaperone systems, as well as AAA+ protease systems. We want to understand how the stress response of the B. subtilis cells is orchestrated and what the role of the interplay of the different chaperone and protease systems in that response is.

The proteolytic arm of the PQS entails AAA+ protease complexes, such as ClpCP, ClpXP, and ClpEP but also the AAA+ proteases Lon or FtsH. These complexes can facilitate the general proteolysis of unfolded, misfolded and/or damaged proteins, which otherwise cannot be rescued or repaired by the chaperones. These AAA+ protease complexes can also be involved in regulatory proteolysis, by controlling e.g. the activity and stability of key transcription factors.

The substrate recognition and selection of the AAA+ proteins which are unfoldases often depends on their interaction with different adaptor proteins that can recognize and target substrate proteins to the AAA+ unfoldase such as ClpC. The activity of these adaptor proteins can also be regulated. One of the known adaptor proteins is the protein arginine kinase McsB, whose activity is induced by McsA and counteracted by the phosphatase YwlE.

In the presence of the associated ClpP protease complex the unfolded substrate protein can be transferred for degradation by the ClpP protease complex. However, in the absence of ClpP, the same substrate protein can also refold, when released, allowing a possible switch between protein repair and removal.

The central role of the AAA+ proteins in bacterial physiology was confirmed by the identification of ClpC as an antibiotic target in Mycobacterium tuberculosis and consistent with this discovery specific toxic mutations in AAA+ proteins such as ClpC were identified.

  1.  We are currently investigating the interplay of chaperones and proteases, utilizing whole genome and proteome approaches with gene deletion and CRSPRi libraries.
  2.  We are evaluating the role, function and interplay of different ClpC adaptor protein and could identify McsB as the adaptor protein necessary to remove heat stress induced protein aggregates. Therefore, we are investigating the role of McsB and protein arginine phosphorylation in protein homeostasis, both in vivo and in vitro. This project also includes the assessment of the role of the interaction of ClpC with ClpP in the aggregate removal and experiments to understand a possible decision between aggregate removal by repair or degradation.
  3. In another project we are investigating ClpC as target for antibiotics and try to understand how the toxic ClpC variants can lead to cell death, utilizing proteomic and genomic approaches.

 

Heat stress and stringent response

In the framework of a collaborative research program "Nucleotide Second Messenger Signaling in Bacteria" by the DFG (SPP 1879) we are investigating the role of (p)ppGpp and the stringent response during heat shock response and how this alarmone can limit and modulate translation. Here we are also applying genome-wide screening to identify proteins involved in (p)ppGpp response during heat shock and other stresses.

 

Biofilm

During the biofilm formation of B. subtilis cells, specific matrix compounds are synthesized and secreted. The proteinaceous compound is the TasA protein, which switches after secretion into an amyloid-like structure that forms fibrils stabilizing the extracellular biofilm matrix. Together with the group of Hartmut Oschkinat at the Leibniz Forschungsinstitut für Molekular Pharmakologie (FMP, Berlin) and structural biologists of the Heinemann Lab at the Max Delbrück Center for Molecular Medicine (MDC, Berlin), we are investigating biofilm formation and the switch of soluble TasA into the fibril forming amyloid-like structure.

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