Group Elif Karagöz

Protein Quality Control in the Endoplasmic Reticulum

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The Question

A healthy proteome is critical for every organism. Cells constantly need to monitor their proteins and respond to physiological and pathological conditions that perturb the delicate balance between protein synthesis, folding and degradation. In the endoplasmic reticulum (ER), the protein-folding homeostasis is surveyed by a conserved signaling network called the unfolded protein response (UPR). The main purpose of the UPR is to adjust the ER’s folding capacity. How sensors and transducers detect protein-folding problems and mount an appropriate response is a major open question.

The Approach

In my lab, we seek to understand the UPR at a mechanistic level. We combine cell biology and biochemistry to dissect how cells maintain a protein-folding homeostasis in the ER. Using next generation sequencing and proteomic approaches, we obtain global information on the molecular components regulating ER-quality control. We then reconstitute these processes biochemically and apply structural methods to dissect their working principles at atomic resolution. Our long-term goal is to use the mechanistic insights derived from these approaches to restore protein homeostasis in variety human diseases caused by protein misfolding.

Elif Karagöz

Elif Karagöz majored Molecular Biology and Genetics with a minor in Chemistry at the Middle East Technical University in Turkey. She got her Master’s degree in Molecular Biology at the Max Planck Research School in Göttingen. After completing her PhD at Utrecht University in the group of Stefan Rüdiger, she did a postdoc at Peter Walter’s lab at the University of California San Francisco.

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Main Building
Room: 3.609

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Spotlights

Sensing protein-folding perturbations in the ER

The UPR sensors directly detect unfolded proteins accumulating in the ER as activating ligands. ER-chaperones also bind the UPR sensors and regulate their activation/deactivation dynamics. In my lab, we dissect how the interplay among unfolded proteins, sensors and chaperones tunes the UPR using biochemical, structural, and cell biology approaches.

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Tuning protein flux into the endoplasmic reticulum

Protein synthesis and folding is tightly coupled to allow error-free assembly of the proteome. Posttranscriptional regulation provides rapid and reversible means for tuning protein synthesis, yet the mechanisms regulating the fate of ER-targeted mRNAs during protein folding stress remain largely unknown. To this end, we aim to reveal how translation and stability of ER-targeted mRNAs are regulated to maintain ER homeostasis.

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    Team

    Aleksandra Anisimova
    PhD Student
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    Room: 3.502

    Sascha Gratzl
    PhD Student
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    Room: 3.507

    Arda Kara
    Bachelor Student
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    Room: 3.507

    Elif Karagöz
    Group Leader
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    Room: 3.609

    Noah Meister
    Master Student
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    Room: 3.507

    Milica Mihailovic
    PhD Student
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    Room: 3.502

    Anastasia Okun
    PhD Student
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    Room: 3.507

    Sabina Omerbegovic
    Scientist
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    Room: 3.507

    Grzegorz Scibisz
    PhD Student
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    Room: 3.507

    Selected Publications

    IGF2BP1 phosphorylation in the disordered linkers regulates ribonucleoprotein condensate formation and RNA metabolism.

    2024 Nature communications;15(1):9054.
    PMID:  39426983

    Hornegger Harald, Anisimova Aleksandra S, Muratovic Adnan, Bourgeois Benjamin, Spinetti Elena, Niedermoser Isabell, Covino Roberto, Madl Tobias, Karagöz G Elif

    Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering.

    2024 The EMBO journal;43(20):4668, 4698, 4668-4698.
    PMID:  39232130

    Kettel Paulina, Marosits Laura, Spinetti Elena, Rechberger Michael, Giannini Caterina, Radler Philipp, Niedermoser Isabell, Fischer Irmgard, Versteeg Gijs A, Loose Martin, Covino Roberto, Karagöz G Elif

    Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy.

    2023 The EMBO journal;42(10):e112053.
    PMID:  36762703

    Picchianti Lorenzo, Sánchez de Medina Hernández Víctor, Zhan Ni, Irwin Nicholas At, Groh Roan, Stephani Madlen, Hornegger Harald, Beveridge Rebecca, Sawa-Makarska Justyna, Lendl Thomas, Grujic Nenad, Naumann Christin, Martens Sascha, Richards Thomas A, Clausen Tim, Ramundo Silvia, Karagöz G Elif, Dagdas Yasin

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