Hsp104 and ClpB are hexameric ATPases that resolubilize aggregated proteins in collaboration with the Hsp70 chaperone system. Hsp104/ClpB functionally interact only with their respective Hsp70 system and this specificity is mapped to the Hsp104/ClpB coiled-coil domain (CCD). We hypothesize that the interaction between Hsp70 and Hsp104/ClpB CCD stimulates nucleotide exchange and release of substrate from Hsp70. In the current study, the CCDs of E. coli ClpB and S. cerevisiae Hsp104 have been purified. Isolated domains are monomeric and well folded. They inhibit refolding of aggregated firefly luciferase in a species-specific manner. We found that the ATPase activity of E. coli DnaK is stimulated at low concentrations of the E. coli ClpB CCD but not by yeast Hsp104 CCD. However, in another bacterial system (Thermus thermophilus) we found that the ClpB CCD inhibits The ATPase activity of DnaK suggesting that the interaction may have different consequences in distinct chaperone networks.

Este trabalho iniciou-se com o objetivo de superexpressar proteínas com atividade ATPase, como tentativa de alterar a conservação de energia livre na levedura S. cerevisiae, de maneira a aumentar o rendimento da fermentação alcoólica. Para isso, duas ATPases nativas de S. cerevisiae, as chaperonas codificadas pelos genes HSP104 e CDC48, foram superexpressas, individualmente, sob o controle de quatro promotores de diferentes forças, provocando diferentes gastos energéticos na levedura. Entretanto, não foi possível obter aumento no rendimento em etanol. Em seguida, foi feito um estudo que visou comparar essas linhagens em situação de estresse térmico, ácido ou osmótico, tipicamente encontrados no processo brasileiro de produção de etanol. A 40 °C, uma linhagem superexpressando CDC48 apresentou velocidade específica máxima de crescimento 17 % maior que a linhagem de referência, indicando maior tolerância ao estresse térmico. Finalmente, avaliou-se Hsp104 e Cdc48 em um contexto fisiológico no qual as atividades dessas proteínas pudessem ser mais requeridas. Como as chaperonas moleculares são conhecidas por agirem como primeira linha de defesa contra a formação de proteínas incorretamente enoveladas e agregados proteicos, estudaram-se a morfologia e a fisiologia da superexpressão de HSP104 e CDC48 em linhagens com desarranjo no controle de qualidade de proteínas intracelulares, causado por mutações no proteassomo 20S. A superexpressão de CDC48 ou HSP104 reverteu em parte a morfologia alterada de alguns desses mutantes de proteassomo. / The initial goal of this work was to overexpress proteins with ATPase activity in Saccharomyces cerevisiae, as an attempt to alter the conservation of free energy in this yeast, in order to increase alcoholic fermentation yield. Therefore, two native S. cerevisiae ATPases, the chaperones encoded by HSP104 and CDC48, were individually overexpressed under the control of four promoters with different strengths, in order to provoke different levels of energy expenditure. Increments in the ethanol yield could not be observed in any of the constructed strains. Subsequently, a study was carried out to compare these mutant strains with reference strains under heat, acid or osmotic stress, which are typically found in the industrial fuel ethanol production in Brazil. At 40 oC a strain overexpressing CDC48 displayed a maximum specific growth rate 17 % higher than that of the reference strain, indicating a greater tolerance to heat stress. Finally, Hsp104 and Cdc48 were evaluated in a physiological context in which the activity of these proteins would be required in a higher level. Since molecular chaperones are known to act as the first defense line against the formation of misfolded proteins and aggregates, the physiological and morphological effects of HSP104 or CDC48 overexpression were analyzed in strains with protein quality control disarrangements caused by mutations in proteasome 20S. The overexpression of either CDC48 or HSP104 partially reversed the altered morphology of some of these proteasome mutants.

Este trabalho iniciou-se com o objetivo de superexpressar proteínas com atividade ATPase, como tentativa de alterar a conservação de energia livre na levedura S. cerevisiae, de maneira a aumentar o rendimento da fermentação alcoólica. Para isso, duas ATPases nativas de S. cerevisiae, as chaperonas codificadas pelos genes HSP104 e CDC48, foram superexpressas, individualmente, sob o controle de quatro promotores de diferentes forças, provocando diferentes gastos energéticos na levedura. Entretanto, não foi possível obter aumento no rendimento em etanol. Em seguida, foi feito um estudo que visou comparar essas linhagens em situação de estresse térmico, ácido ou osmótico, tipicamente encontrados no processo brasileiro de produção de etanol. A 40 °C, uma linhagem superexpressando CDC48 apresentou velocidade específica máxima de crescimento 17 % maior que a linhagem de referência, indicando maior tolerância ao estresse térmico. Finalmente, avaliou-se Hsp104 e Cdc48 em um contexto fisiológico no qual as atividades dessas proteínas pudessem ser mais requeridas. Como as chaperonas moleculares são conhecidas por agirem como primeira linha de defesa contra a formação de proteínas incorretamente enoveladas e agregados proteicos, estudaram-se a morfologia e a fisiologia da superexpressão de HSP104 e CDC48 em linhagens com desarranjo no controle de qualidade de proteínas intracelulares, causado por mutações no proteassomo 20S. A superexpressão de CDC48 ou HSP104 reverteu em parte a morfologia alterada de alguns desses mutantes de proteassomo. / The initial goal of this work was to overexpress proteins with ATPase activity in Saccharomyces cerevisiae, as an attempt to alter the conservation of free energy in this yeast, in order to increase alcoholic fermentation yield. Therefore, two native S. cerevisiae ATPases, the chaperones encoded by HSP104 and CDC48, were individually overexpressed under the control of four promoters with different strengths, in order to provoke different levels of energy expenditure. Increments in the ethanol yield could not be observed in any of the constructed strains. Subsequently, a study was carried out to compare these mutant strains with reference strains under heat, acid or osmotic stress, which are typically found in the industrial fuel ethanol production in Brazil. At 40 oC a strain overexpressing CDC48 displayed a maximum specific growth rate 17 % higher than that of the reference strain, indicating a greater tolerance to heat stress. Finally, Hsp104 and Cdc48 were evaluated in a physiological context in which the activity of these proteins would be required in a higher level. Since molecular chaperones are known to act as the first defense line against the formation of misfolded proteins and aggregates, the physiological and morphological effects of HSP104 or CDC48 overexpression were analyzed in strains with protein quality control disarrangements caused by mutations in proteasome 20S. The overexpression of either CDC48 or HSP104 partially reversed the altered morphology of some of these proteasome mutants.

Yeast prions e.g. [PSI+], [PIN+] and [URE3] are similar to mammalian amyloids that cause neurodegenerative diseases. [PSI+] is the aggregated self-perpetuating (prion) isoform of Sup35, a translation termination factor. The molecular chaperone Hsp104 plays a crucial role in the maintenance and propagation of [PSI+]. Deletion of the GET2 gene has been shown to cause a [PSI+] curing defect by excess Hsp104 and [PSI+] instability on synthetic medium (S. Muller, J. Patterson and Y. Chernoff, unpublished data; and J. Patterson Honors Thesis). Get2 is a membrane protein working in a complex with Get1 and Get3 proteins. This complex, called GET (Golgi-to-ER Traffic), is known to retrieve resident ER proteins from Golgi. In this particular study we provide further evidence for the connection between the GET pathway and yeast prions. The get2 deletion also leads to a detectable loss of [PIN+] prion on synthetic medium. The role of the other two members of the Get complex in prion propagation is also explored. The levels and the activity of Hsp104 in the get2 mutants is analyzed. The size of [PSI+] aggregates in the get2Δ strain is compared to that found in wild type. Finally, other possible mechanisms for the effect of get2 on prion maintenance and propagation are addressed.

Organisms are frequently exposed to fluctuating environmental conditions and might consequently experience stress. Environmental stress can damage cellular components, which can threaten especially single-celled organisms, such as yeast, as they cannot escape. To survive, cells mount protective stress responses, which serve to preserve cellular components and architecture. Recent findings in yeast show that the stress response upon energy depletion stress involves a gelation of the cytoplasm due to macromolecular protein assembly, characterized by drastic changes in cytoplasmic material properties. Remarkably, the stress-induced cytoplasmic gelation is protective, raising the question whether this could be a common strategy of cells to cope with severe stress. I hypothesized that protein aggregation induced by another common stress, severe heat shock, might cause a similar cytoplasmic gelation in yeast. Furthermore, I hypothesized that the reversibility of cytoplasmic gelation is provided by molecular chaperones, which are known regulators of protein aggregation. In this thesis, I therefore aimed to characterize the changes in the material properties of the cytoplasm upon severe heat shock as well as their underlying causes and how molecular chaperones affect these changes. To characterize heat-induced changes in the material properties of the cytoplasm, I monitored Schizosaccharomyces pombe cells during recovery from severe heat shock using a combination of cell mechanical assays, time-lapse microscopy and single-particle tracking. I found that the cells entered a prolonged growth arrested state upon stress, which coincided with significant cell stiffening and a long-range motion arrest of lipid droplets in the cytoplasm, while smaller cytoplasmic nanoparticles remained mostly mobile. At the same time, a significant fraction of proteins aggregated in the cytoplasm, forming insoluble inclusions such as heat shock granules. After stress cessation, the observed changes were reversed as stiffened cells softened and lipid droplets resumed long-range motion. Cell softening and lipid droplet motion recovery coincided with protein disaggregation. These processes could be delayed by impairing protein disaggregation through genetic perturbation of the molecular chaperone Hsp104, which functions as a protein disaggregase. In contrast, no influence on protein disaggregation or heat-induced cytoplasmic material property changes was detected for the small heat shock protein Hsp16. These results suggest that the cytoplasm gels upon severe heat shock due to protein aggregation and is refluidized during recovery with the help of Hsp104. Remarkably, cells resumed growth only after refluidization of the cytoplasm, suggesting that reversible cytoplasmic gelation may contribute to regulation of the heat-induced growth arrest. In addition, cytoplasmic gelation could potentially preserve cellular architecture during heat shock. Overall, the results from my thesis work indicate that reversible cytoplasmic gelation due to macromolecular protein assembly may be a universal cellular response to severe stress which is associated with a stress-protective growth arrest. A likely stress-specific part of this response is the chaperone-dependent refluidization of the cytoplasm, which might explain the prolonged growth arrest seen upon severe heat shock as compared to other stresses and might allow more time for the repair of heat-induced damage.:Abstract Zusammenfassung Table of contents Figure index List of abbreviations 1 Introduction 1.1 Heat shock affects cellular function and fitness 1.1.1 Cells respond to stress in phases 1.1.2 Heat shock threatens cellular homeostasis and structural integrity 1.1.3 Stress severity determines detrimental effects of heat shock 1.1.4 Heat stress causes protein aggregation 1.1.5 Heat shock granules are functional aggregates in yeast 1.2 The heat shock response protects cellular fitness 1.2.1 Cells change transcription to adapt to stress 1.2.2 Molecular chaperones are important in stress protection 1.2.3 Hsp104 is a protein disaggregase chaperone 1.2.4 Small heat shock proteins modulate protein aggregation 1.2.5 Stress severity determines modules of the heat shock response 1.3 Cytoplasmic material properties change during stress 1.3.1 Cells homeostatically adapt cytoplasmic material properties during stress 1.3.2 The cytoplasm is viscoelastic 1.3.3 Is the cytoplasm a gel? 1.3.4 Stress can induce cytoplasmic gelation 1.4 Research aims 2 Materials and Methods 2.1 S. pombe strains and growth conditions 2.1.1 Growth conditions 2.1.2 Construction of S. pombe strains 2.1.3 S. pombe transformation 2.1.4 S. pombe colony PCR 2.1.5 S. pombe strains used in this thesis 2.2 Plasmids and cloning 2.2.1 Plasmids used in this thesis 2.2.2 Construction of plasmid for fluorescent GEM nanoparticle expression 2.2.3 E. coli transformation 2.2.4 Plasmid purification from E. coli 2.3 S. pombe stress treatments 2.3.1 Heat shock treatment 2.3.2 Osmoadaptation 2.4 Cell biological methods 2.4.1 Viability assay 2.4.2 Growth assay 2.5 Cell bulk mechanical assays 2.5.1 Spheroplasting assay 2.5.2 Atomic force microscopy 2.5.3 Real-time deformability cytometry 2.5.4 RT-DC sample preparation 2.5.5 RT-DC setup and measurements 2.5.6 RT-DC data evaluation 2.6 Microscopy 2.6.1 Microscopy of GEM particles 2.6.2 Fluorescence microscopy of endogenously labeled Pabp-mCherry 2.6.3 Microscopy of µNS particles 2.7 Image analysis 2.7.1 Image analysis of Pabp-mCherry in vivo fluorescence microscopy 2.7.2 Differenced brightfield image analysis 2.7.3 Kymographs 2.8 Single-particle tracking analysis 2.8.1 Particle tracking 2.8.2 Mean squared displacement analysis 2.9 Optical diffraction tomography (ODT) 2.9.1 ODT sample preparation 2.9.2 ODT optical setup and measurements 2.9.3 ODT tomogram reconstruction and quantitative analysis 2.10 Lysis and sedimentation assay 2.10.1 Lysis buffer 2.10.2 S. pombe heat shock treatment and lysis 2.10.3 Sedimentation assay 2.10.4 Protein concentration measurement 2.10.5 SDS-PAGE 2.10.6 Coomassie staining 2.10.7 Western Blot 3 Results 3.1 Physical and chemical conditions affect heat shock survival and heat-induced growth arrest of S. pombe 3.1.1 S. pombe arrests growth during severe heat shock 3.1.2 Heat-induced growth arrest is dose-responsive 3.1.3 Heat-induced growth arrest depends on experimental conditions 3.1.4 Buffer pH and energy source have a strong impact on heat shock survival 3.1.5 Osmoadaptation protects cells during heat shock 3.2 Severe heat shock induces reversible cellular stiffening 3.2.1 Cellular rounding upon cell wall removal is delayed after heat shock 3.2.2 Elastic modulus of S. pombe cells is increased after heat shock 3.2.3 Recovery from heat-induced growth arrest is preceded by cell softening 3.3 Long-range particle dynamics in cytoplasm are abolished after heat shock 3.3.1 Small particle dynamics are largely independent of heat shock treatment 3.3.2 Lipid droplets are confined in space after heat shock 3.4 Cytoplasmic crowding increases during heat shock 3.5 Heat shock induces reversible protein aggregation 3.5.1 Insoluble protein fraction is increased after heat shock 3.5.2 Heat shock granules form reversibly during heat shock 3.5.3 HSG formation and dissolution are correlated with changes in cytoplasmic long-range dynamics 3.6 Molecular chaperones modulate cytoplasmic material property changes during heat stress recovery 3.6.1 Hsp104 but not Hsp16 is required for disaggregation of heat shock granules 3.6.2 Hsp104 but not Hsp16 is required for recovery from heat-induced growth arrest 3.6.3 Hsp104 but not Hsp16 is required for recovery of cytoplasmic long-range dynamics 3.6.4 Hsp104 but not Hsp16 is required for rapid reversal of cellular stiffening which coincides with growth recovery 4 Discussion 4.1 Summary and model 4.2 Which mechanism underlies cell stiffening upon heat shock? 4.2.1 Heat-induced protein aggregation might cause cell stiffening 4.2.2 Heat-induced protein aggregation might lead to cytoplasmic gelation 4.2.3 Many factors could contribute to protein aggregation and cytoplasmic gelation 4.3 The heat-induced growth arrest state is associated with reversible cytoplasmic gelation 4.3.1 Cytoplasmic material property changes mark the severe heat-induced growth arrest state 4.3.2 Is cytoplasmic gelation a common response to severe stress? 4.4 What are the biological consequences of cytoplasmic gelation? 4.4.1 Cytoplasmic gelation might obstruct processes that require motion of large structures 4.4.2 Is cytoplasmic gelation upon heat shock protective? 4.5 Heat shock recovery involves the chaperone-mediated refluidization of the cytoplasm 4.5.1 Cytoplasmic refluidization is required for growth recovery 4.5.2 Stress tolerance is marked by enhanced reversibility of cytoplasmic gelation 4.5.3 The protein disaggregase chaperone Hsp104 regulates the reversal of heat-induced cytoplasmic material property changes 4.6 Conclusion References Acknowledgements Publications and Contributions 5 Erklärung entsprechend §5.5 der Promotionsordnung