Turgay Research Projects

Protein homeostasis, stress and stringent response

In our laboratory, we investigate protein homeostasis in Bacillus subtilis, especially under stress conditions. B. subtilisencodes highly conserved chaperone and AAA+ protease systems in its cellular protein quality control network. AAA+ protease complexes like ClpCP, ClpXP, and ClpEP can facilitate the proteolysis of unfolded, misfolded, or damaged proteins. These AAA+ protease complexes can also be involved in regulatory proteolysis, by controlling, e.g. the activity and stability of key transcription factors. The recognition and selection of substrates by the AAA+ proteins, which are unfoldases, often depend on their interaction with different adaptor proteins that can recognize and target substrate proteins to the hexameric AAA+ unfoldase, such as ClpC. In the presence of the associated ClpP protease complex, the unfolded substrate protein can be transferred for degradation to the protease complex.

We have identified the arginine kinase McsB, which is induced by McsA and modulated by the phosphatase YwlE, as the ClpC adaptor protein, essential for removing heat-stress-induced protein aggregates. We are continuing to investigate this unusual chaperone system and its interplay with protein arginine phosphorylation, which enables disaggregation and refolding, or disaggregation and degradation.

We frequently collaborate with other research groups on newly discovered aspects of ClpCP functions. We are investigating ClpCP as an antibiotic target, characterizing toxic ClpC mutants, and exploring the role of endogenous and phage adaptor proteins that reprogram ClpCP for protein degradation during spore formation (MfdA) or bacteriophage lysis (Gp53).

We observed that the stress response transcription factor Spx, which activates redox chaperones, can simultaneously inhibit translation-related genes. In addition, B. subtilis cells also inhibit translation upon protein folding stress, mediated by the heat-inducible second messenger pppGpp. This suggests that downshifting translation during protein folding stress is crucial for the heat shock response, as newly synthesized proteins would overload the cellular protein quality control system.

Recently, we developed a fitness-based genetic screen to identify new genes involved in heat shock, the stringent response, and other stress response pathways. We discovered genes encoding proteins of the Y-complex that control the activity of the endonuclease RNaseY, modulating RNA stability and gene expression. This protein complex is also necessary to initiate ribosome degradation during nutrient starvation or protein folding stress, extending the downregulation of translation to the removal of abundant ribosomes.