Multiple Designer Organelles for Expanded Eukaryotic life

Project Information

MultiOrganelleDesign

Grant agreement ID: 883687

DOI

10.3030/883687

EC signature date 29 May 2020

Start date 1 January 2022

End date 31 December 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 499 068,00

EU contribution

€ 2 499 068,00

Coordinated by

JOHANNES GUTENBERG-UNIVERSITAT MAINZ
Germany

Periodic Reporting for period 2 - MultiOrganelleDesign (Multiple Designer Organelles for Expanded Eukaryotic life)

Reporting period: 2023-07-01 to 2024-12-31

Summary of the context and overall objectives of the project

Creating specialized structures inside cells was a key milestone in the development of complex life. In our research on "MultiOrganelleDesign," we create new structures inside cells to perform specialized tasks, such as producing proteins with unique features. Our goal is to design organelles that can carry out the main processes of life—like reading DNA, RNA and making proteins—inside cells, but in a customizable way.
This allows us to explore new ways to engineer living systems with multiple custom genetic codes. These organelles will be fine-tuned to handle specific tasks, such as processing RNA or breaking down targeted proteins. Beyond the scientific interest, this work could help develop new proteins, materials, and biotechnologies with unique properties.
We also aim to create more precise labeling methods than current fluorescent technologies, allowing us to label proteins with single-residue accuracy. Our approach is flexible and can be adapted to design customized proteins, RNA, and genetic codes with non-standard functions.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have successfully designed membrane-less and thin-film organelles within living eukaryotic cells, enabling them to carry multiple genetic codes. This work demonstrates the principles of how phase separation can be used to spatially segregate novel functionalities within eukaryotic cells. Beyond deepening our fundamental understanding of how intrinsically disordered proteins (IDPs) can achieve complex functionality, this research provides a new platform for engineering cellular mechanisms in eukaryotes.
In a major milestone, we developed an in situ labeling method to visualize the conformation of IDPs within functional nuclear pore complexes (NPCs) for the first time. The paper by Miao et al. consolidates our lab’s expertise in chemical biology, synthetic biology, designer organelle engineering, high-resolution fluorescence tool development, and microscope engineering into one comprehensive achievement. In collaboration with molecular dynamics simulations conducted by the Hummer lab, we produced the first experimentally validated molecular movie of the NPC, resolving the ~50 MDa disordered proteins, which, even in the highest resolution electron tomograms, previously appeared only as voids.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Genetic code expansion is a powerful tool in protein translational engineering. To introduce a specific site modification, the relevant codon must be altered in either the DNA or RNA sequence. Recently, we filed a patent application demonstrating that our protein organelle concept can also be applied to engineer codons within RNA (EP 24183463.9).
• Patent: E. A. Lemke, Schartel L. “Nucleic Acid Molecule Complex for Targeted Pseudouridylation in Mammalian Cells” (2024).
As we move forward, we expect to further enhance the functionality of engineered organelles, bringing us closer to realizing the full potential of synthetic biology in tailoring living systems with unprecedented capabilities.

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