PhD project

Supervisor: Pedro Carvalho

Accumulation of misfolded proteins and aberrant protein aggregates are hallmarks of a wide range of pathologies such as neurodegenerative diseases and cancer. Under normal conditions, these potentially toxic protein species are kept at low levels due to a variety of quality control mechanisms that detect and selectively promote their degradation. Our lab investigates these protein quality control processes with a particular focus on ER-associated degradation (ERAD), that looks after membrane and secreted proteins. The ERAD pathway is evolutionarily conserved and in mammals, targets thousands of proteins influencing a wide range of cellular processes, from lipid homeostasis and stress responses to cell signaling and communication.

We investigate the mechanisms of ERAD using multidisciplinary approaches both in human and yeast cells. We are using CRISPR-based genome-wide genetic screens and light microscopy experiments to identify and characterize molecular components involved in the degradation of disease-relevant toxic proteins. In parallel, we use biochemical and structural approaches to dissect mechanistically the various steps of the ERAD pathways. These strategies helped us in discovering ERAD mechanisms contributing to the homeostasis of the endoplasmic reticulum, the organization of the nuclear envelope and regulation of lipid metabolism. Although we focus primarily on fundamental aspects of protein quality control, our work will shed light on how these processes are disrupted in human disease and may ultimately contribute to better therapeutics.

Publications:

• Krshnan L, Siu WS, Van de Weijer M, Hayward D, Guerrero EN, Gruneberg U, Carvalho P. (2022) Regulated degradation of the inner nuclear membrane protein SUN2 maintains nuclear envelope architecture and function. eLife 10.7554/eLife.81573
• Klug Y, Deme J, Corey R, Renne M, Stansfeld P, Lea S, Carvalho P. (2021) Mechanism of lipid droplet formation by the yeast Sei1/Ldb16 Seipin complex. Nat Commun.
• Ferreira J, Carvalho P. (2021). Pex30-like proteins function as adaptors at distinct ER membrane contact sites. J Cell Bio.
• van de Weijer M, Krshnan L, Liberatori S, Guerrero EN, Robson-Tull J, Hahn L, Lebbink RJ, Wiertz E, Fischer R, Ebner D, Carvalho P (2020). Quality Control of ER Membrane Proteins by the RNF185/Membralin Ubiquitin Ligase Complex. Mol Cell.
• Natarajan N, Foresti O, Wendrich K, Stein A, Carvalho P. (2020) Quality Control of Protein Complex Assembly by a Transmembrane Recognition Factor. Mol Cell.
• Ruggiano A, Mora G, Buxó L, Carvalho P. (2016) Spatial control of lipid droplet proteins by the ERAD ubiquitin ligase Doa10. EMBO J.
• – Foresti O, Rodriguez-Vaello V, Funaya C, Carvalho P. (2014) Quality control of inner nuclear membrane proteins by the Asi complex. Science.
• Stein A, Ruggiano A, Carvalho P, Rapoport TA. (2014) Key Steps in ERAD of Luminal ER Proteins Reconstituted with Purified Components. Cell.