1. Research Background:

Cellular differentiation, developmental processes, and environmental factors challenge the integrity of the proteome in every eukaryotic cell. The maintenance of protein homeostasis, or proteostasis, involves the degradation of misfolded and damaged proteins, and is essential for cellular function, organismal growth, and ultimately viability. Sustaining proteostasis is not only a long-term challenge for individual cells but also for entire organisms, since damaged proteins accumulate with stress and ageing. It is commonly thought that age-related impairment of proteostasis affects general quality control networks, causing enhanced aggregation of misfolded proteins that can be toxic for cells and shortens organismal lifespan. Not all tissues are equally susceptible to the toxicity of protein aggregates, suggesting tissue-specific differences in proteostasis pathways. In humans, aberrant protein aggregation is often associated with neurodegeneration in age-dependent disorders such as Alzheimer’s and Parkinson’s diseases.

The ubiquitin/proteasome system (UPS) is a major proteolytic route functioning in a cellular network that helps to maintain the proteome during stress and ageing. Degradation of damaged proteins is mediated by the 26S proteasome upon attachment of ubiquitin proteins. Another proteolytic system supporting proteostasis is the autophagy-lysosome pathway that degrades proteins inside activated autophagosomes. An age-related impairment of either of these systems causes enhanced protein aggregation and affects lifespan, reflecting functional overlap and cooperation between UPS and autophagy in stress and ageing. The ultimate goal of our research is to assemble a global picture of stress-induced proteolytic networks critical for ageing and neurodegeneration. We address both cellular and organismal regulation of protein degradation pathways using the powerful genetic model of Caenorhabditis elegans.

2. Research questions addresses by the group:

Proteostasis is achieved via a conserved network of quality control pathways that support the generation of correctly folded proteins, prevent proteins from misfolding, and remove potentially harmful protein species. However, the proteostasis network has a limited capacity and its impairment causes protein aggregation that deteriorates both cellular and organismal viability. Recent studies identified cell-nonautonomous regulation of proteotoxic stress response, suggesting the existence of intricately balanced proteostasis networks important for integration and maintenance of the organismal proteome. Our research particularly aims to understand the dynamic regulation ofproteolytic pathways that integrate environmental and physiological changes. The detailed analysis of both cellular and tissue-related coordination of proteostasis will allow us to assemble a global picture of conserved protein degradation networks important to safeguard theorganismal proteome in health and disease. Our lab aims to unravel the interplay between proteolytic networks at the molecular, cellular, and organismal level and to define adaptation mechanisms that ensure its integrity in response to environmental stress conditions or inherited, disease- associated mutations. The central research program is focused on the following points:

• Proteostasis mechanisms important for ageing and age-related diseases
• Cell-autonomous regulation of protein quality control
• Interorgan communication in sensory perception and ageing
• Pathomechanisms underlying disease-related dysfunction

3. Possible project(s):

Current projects address physiological aspects of protein turnover in the context of ageing- associated processes, such as muscle development and regeneration, genome stability, mitochondrial metabolism, and protein aggregation. Therefore, we combine innovative in vitro and in vivo protein degradation assays, microscopical, optogenetic, and chemosensory methods, which allow the identification and characterization of conserved proteostasis mechanisms. In addition to intracellular proteostasis networks we address cell- nonautonomous proteostasis pathways regulated by paracrine signals. Our most recent work unraveled how the smell of food sensed via a single pair of olfactory neurons affects physiology and ageing. We aim to understand the functional role of protein degradation in the context of ageing-associated diseases. Our long-term goal is to define the crosstalk between stress-induced proteostasis networks and ageing, which will help to identify conserved diseases mechanisms.

4. Applied methods and model organisms:

The long-term objective of this project is to define proteostasis networks essential for stress resistance and tissuefunctionality. This innovative and interdisciplinary research program will combine state-of-the-art transcriptome/proteome analyses with opto- and chemical-genetics approaches, manipulation and measuring ofneuronal signaling/activity along with large-scale genetic screenings to identify and characterize regulatory circuits modulating proteostasis. The conserved regulation of proteostasis networks will be studied in C. elegans, mammalian cell culture, and samples of disease-patients. Besides novel insights into sensory adaptation mechanisms this research project will set the ground to tackle the pathophysiology of age-associated diseases. Mechanistic insights into the crosstalk between metabolic changes, stress signals, and ubiquitin-dependent regulation will help to develop new therapeutic strategies for metabolic and neurodegenerative diseases. The model organism C. elegans allows an ideal combination of genetic, biochemical and in vivo imaging techniques to examine the dynamic cross talk between sensory perception and proteostasis networks. Over the last years weestablished innovative degradation assays that allow to follow protein turnover in vivo. These assays were successfully used in genetic screens; subsequent whole genome sequencing/mapping techniques helped to find for example a new crosstalk between mitochondrial metabolism and cytosolic protein degradation pathways. In most projects we were able to transfer the findings made in nematodes into human cell culture models, which are often related to age-associated diseases.

5. Desirable skills and qualifications:

We are seeking a highly motivated PhD student to join our enthusiastic and collaborative group. Successful applicants should have a solid background in molecular biology and experience in cell biology, genetics, or biochemistry. Candidates should have demonstrated outstanding performance through their undergraduate studies. Besides creativity, a strong ability for problem solving through analytical thinking combined with an enthusiasm for scientific research is highly desirable. Additionally, we expect good communication skills, fluent English, and the ability for teamwork.

6. References:

1. Finger F., Ottens F., Springhorn A., Drexel T., Proksch L., Metz S., Cochella L., Hoppe T. (2019). Olfaction regulates organismal proteostasis and longevity via miRNA-dependent signaling. Nature Metabolism 1, 350–59.
2. Tawo R., Pokrzywa W., Kevei E., Akyuz M.E., Balaji V., Arian S., Höhfeld J., Hoppe T. (2017). The ubiquitin ligase CHIP integrates proteostasis and aging by regulation of insulin receptor turnover. Cell 169, 470-482.
3. Franz A., Pirson P.A., Pilger D., Halder S., Achuthankutty D., Ramadan K., Hoppe T. (2016). Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression. Nat Commun. 7, 10612.
4. Segref A., Kevei E., Pokrzywa W., Schmeisser K., Mansfeld J., Livnat-Levanon N., Ensenauer R., Glickman M.H., Ristow M., Hoppe T. (2014). Pathogenesis of human mitochondrial diseases is modulated by reduced activity of the ubiquitin/proteasome system. Cell Metab 19, 642-652.
5. Gazda L., Pokrzywa W., Hellerschmied D., Löwe T., Forné I., Mueller-Planitz F., Hoppe T.*, Clausen T (2013). The myosin chaperone UNC-45 is organized in tandem modules to support myofilament formation in C. elegans. Cell 152: 183-195. (*co-senior author)
6. Franz A., Orth M., Pirson P.A., Sonneville R., Blow J.J., Gartner A., Stemmann O., Hoppe T. (2011). CDC-48/p97 coordinates CDT-1 degradation with GINS chromatin dissociation to ensure faithful DNA replication. Mol Cell. 44, 85-96.
7. Kuhlbrodt K., Janiesch P.C., Kevei E., Segref A., Barikbin R., Hoppe T. (2011). The Machado- Joseph disease deubiquitylase ATX-3 couples longevity and proteostasis. Nat Cell Biol 13, 273- 281.
8. Janiesch P.C., Kim J., Mouysset J., Barikbin R., Lochmüller H., Cassata G., Krause S., and Hoppe T. (2007). The ubiquitin-selective chaperone CDC-48/p97 links myosin assembly to human myopathy. Nat Cell Biol 9, 379-390.
9. Hoppe T., Cassata G., Barral J.M., Springer W., Hutagalung A.H., Epstein H.F., Baumeister R. (2004). Regulation of the Myosin-Directed Chaperone UNC-45 by a Novel E3/E4-Multiubiquitylation Complex in C. elegans. Cell 118, 337-349.
10. Hoppe T., Matuschewski K., Rape M., Schlenker S., Ulrich H.D., Jentsch S. (2000). Activation of a Membrane-Bound TranscriptionFactor by Regulated Ubiquitin/Proteasome-Dependent Processing. Cell 102, 577-586.