Chaperone Systems in Model Organisms

• Main Author: Rizzolo Roustayan, Kamran Daniel
• Format: Dissertation
• Language: English
• Published: ProQuest Dissertations & Theses 01-01-2019
• Subjects: Biochemistry; Bioinformatics; Molecular biology
• ISBN: 108830267X; 9781088302675

Molecular chaperones are typically promiscuous interacting proteins that function globally in the cell for quality control and maintenance of protein homeostasis. They are highly conserved across all organisms. A comprehensive view of their cellular function was obtained through a systematic global integrative network approach. We deciphered interactions involving all core chaperones of Saccharomyces cerevisiae. Our analysis revealed the presence of a large chaperone functional supercomplex encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps, that is central to the topology of the proteome network. Chaperone interactor properties demonstrate preferential protein domains and folds such as the WD40 repeat domain. We further found that many chaperones interact with proteins that form condensates under stress conditions. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities. From an extensive genomic analysis in bacteria we demonstrate the conservation of the close proximity of the tig gene, coding for the ribosome-associated chaperone trigger factor (TF), and the genes coding for the ClpXP proteolytic complex suggesting a possible functional association between the protein folding and the protein degradation systems. The effect of TF on ClpXP-dependent degradation varied depending on the nature of the substrate. For a class of substrates, TF increased the degradation rate. The ClpXP-dependent degradation was enhanced for the λ phage replication protein λO, the master regulator of stationary phase RpoS, and SsrA-tagged proteins by TF in vitro and in vivo. Globally, it is estimated that TF enhances the degradation of about subset of newly synthesized E. coli proteins. Through extensive biochemical and structural analyses, it was found that TF interacts through multiple sites with the ClpX oligomer in a highly dynamic fashion. TF binds the ATPase-domain of ClpX and consequently promotes the movement of the protruding N-terminal zinc binding domain (ZBD) of the chaperone towards the ClpP cylinder. With this movement, TF enhances the degradation of ZBD-bound substrates. These results reveal a novel function of TF as a ClpXP adaptor protein and highlight its broad substrate specificity. This chaperone-protease cooperation constitutes a novel aspect of cellular protein homeostasis.