1. Research Background

Cellular differentiation, developmental processes, and environmental factors challenge the integrity of the proteome in every eukaryotic cell. The maintenance of proteinhomeostasis, 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 aging. 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 neurodegenerationin 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 aging. 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 aging. The ultimate goal of our research is to assemble a global picture of stress-induced proteolytic networks critical for aging and neurodegeneration. We address both cellularandorganismalregulationofproteindegradationpathwaysusingthepowerful genetic model of Caenorhabditis elegans.

2. Research questions addressed 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 of proteolytic 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 the organismal 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 aging and age-related diseases
• Cell-autonomous regulation of protein quality control
• Interorgan communication in sensory perception and aging
• Pathomechanisms underlying disease-related dysfunction

3. Possible project(s):

Current projects address physiological aspects of protein turnover in the context of aging- 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. In our recent work, we found how the smell of food or temperature changes perceived via olfactory or thermosensory neurons affect physiology and aging. We aim to understand the functional role of protein degradation in the context of aging-associated diseases. Our long-term goal is to define the crosstalk between stress-induced proteostasis networks and aging, 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 tissue functionality. This innovative and interdisciplinary research program will combine state-of-the-art transcriptome/proteome analyses with opto- and chemical-genetics approaches, manipulation and measuring of neuronal 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 we established 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 and key publications:

1. Kutzner C.E., Bauer K.C., Lackman J.W., Acton R.J., Sarkar A., Pokrzywa W., Hoppe T. (2024). Optogenetic induction of mechanical muscle stress identifies myosin regulatory ubiquitin ligase NHL-1 in C. elegans. Nat Commun. 15, 6879.
2. Müller L. and HoppeT. (2024). UPS-dependent strategies of protein quality control degradation
   TrendsBiochemSci. doi: 10.1016/j.tibs.2024.06.006.
3. Efstathiou S., Ottens F., Schütter L.S., Ravanelli S., Charmpilas N., Gutschmidt A., Le Pen J., Gehring N.H., Miska E.A., Bouças J., HoppeT.(2022). ER-associated RNA silencing promotes ER quality control. Nat. Cell Biol. 12, 1714-1725.
4. Hoppe T. and Cohen E. (2020). Organismal Protein Homeostasis Mechanisms. Genetics. 215, 889-901.
5. 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.
6. 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.