Nuclear pores in their natural context

MPIB scientists have contributed to deciphering the 3D structure of the nuclear pore of baker's yeast cells.

September 02, 2020

Research group leader Boris Pfander and his team from the Max Planck Institute of Biochemistry, together with colleagues from the Max Planck Institute of Biophysics in Frankfurt am Main and the EMBL in Heidelberg, have investigated the 3D structure of nuclear pores in budding yeast (Saccharomyces cerevisiae). Their results, published in Nature, reveal the architecture of the nuclear pore complex in intact cells and broaden our understanding of crucial processes in life.

Cryo-tomographic slice of a S. cerevisiae cell missing the protein Nup116 kept for 4 hours at the non-permissive temperature of 37°C. Dotted rectangles mark the positions subjected to structural analysis; on the right cryo-EM maps (gray) with fitted the respective integrative models (colored).

Nuclear pores are a highly complex assembly of proteins. Hundreds of them are embedded in the double membrane that surrounds and protects the cell’s nucleus. They act as a gateway that regulates the entry and exit of molecules. An important function of nuclear pores is to regulate the export of a molecule called messenger RNA (mRNA) from the nucleus into the surrounding cell – the cytoplasm – where it delivers instructions for the assembly of proteins.

Revealing the architecture
Now the scientists appreciate better how the nuclear pore works in its native context, how it is maintained and recycled. The study provides a detailed structural description of the three protein rings that make up the nuclear pore, known as the cytoplasmic, nuclear, and inner rings. To show how these rings are arranged in cells, the researchers used a combination of cell biology, computational modelling, and in-cell cryo-electron tomography: an imaging technique, that is used to produce high-resolution 3D views of the molecular landscape inside a cell. This led to fundamental new insights. The scientist found out that the 3D configuration of the cytoplasmic ring accommodates the path of mRNA export.

Understanding the life cycle
The structure of the cytoplasmic ring also serves another function – it exposes a certain part of one nuclear pore protein to the cytoplasm. This domain interacts with proteins that facilitate the process by which nuclear pores are broken down by the cell and replaced with new ones – a process known as autophagic turnover. How exactly the architecture of nuclear pores facilitates the breakdown process – autophagy – and assembly of nuclear pores is largely unknown, but this study provides important first steps towards a better understanding of these mechanisms. With knowledge coming from many different structures, the scientists are closer to understanding how nuclear pores assemble and how the pore evolved from the first cells with a nucleus up to now.

To better understand the assembly of nuclear pores, the researchers grew a yeast strain missing a protein called nucleoporin 116, which plays an important role in the assembly process. The resulting structure was missing the cytoplasmic ring and part of the inner ring. The scientists conclude that these incomplete structures show intermediate states of nuclear pore assembly. Studying this process is important, as failures in the assembly of nuclear pores have been linked to neurodegenerative diseases.

The study yielded detailed structures that scientists from other institutions can use in various ways, for example to study nuclear pore function, how molecules are transported into or out of the nucleus, or how viruses enter the nucleus. Many viruses, such as influenza and HIV, need to get their genetic information past the nuclear pore complex to infect a cell. “It also shows the scientific community that we need to shift scientific efforts towards the investigation of the structure–function relationship of macromolecules directly inside the cell,” says Matteo Allegretti, postdoc in the Beck group and first author of the study. Fundamental processes of life, such as nuclear transport and autophagy, can be understood by combining technologies like cryo-electron tomography with structural modelling, light microscopy, and biochemistry.

Original publication:
M. Allegretti, C.E. Zimmerli, V. Rantos, F. Wilfling, P. Ronchi, H.K.H. Fung, C. Lee, W. Hagen, B. Turoňová, K. Karius, M. Börmel, X. Zhang, C. W. Müller, Y. Schwab, J. Mahamid, B. Pfander, J. Kosinski, M. Beck:
'In-cell architecture of the nuclear pore and snapshots of its turnover', Nature, September 2020
DOI: https://www.nature.com/articles/s41586-020-2670-5

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