Chain length of ceramide in the endoplasmic reticulum membrane is critical for sorting selectivity

Significance 

The cell is the basic unit of life and, at the same time, an extremely complex and sophisticated machine in which thousands of proteins, among other components, are strategically located in different compartments where they carry out cellular functions. The cell must ensure that its proteins are properly distributed to their place of function, because if this fails and they do not reach their destination, the proteins either stop working or get out of control, causing diseases ranging from genetic syndromes to cancer or neurological diseases. Therefore, it is important to investigate how proteins are distributed towards their functional destination.

It was previously suggested that, the lipids that make up the cell membranes may also play an additional role in the distribution of proteins within cells. This work by the Seville researchers solves this enigma of basic biology, demonstrating for the first time how lipids can distribute proteins at the cellular level.

An international team of scientists, coordinated by the Seville Institute of Biomedicine (IBiS) and the University of Seville has solved one of the hitherto unresolved enigmas of basic biology: how exactly do lipids distribute proteins within a cell? To do this, they used a new, completely innovative microscopy technology, which they applied to “mutant” cells they designed in their laboratory. Researchers have observed how lipids distribute proteins within cells, a discovery that could open the door to understanding the causes of protein transport related diseases, such as cancer or neurodegenerative diseases. lipid-based protein cargo sorting into selective export sites in the secretory pathway and reveals the critical importance of the acyl chain length for sorting selectivity. We took advantage of a powerful and cutting-edge microscopy technology called SCLIM to demonstrate in yeast that newly synthesized Gas1-GFP, a major plasma membrane GPI-AP having a very long acyl chain (C26) ceramide lipid moiety, is clustered into discrete ER zones associated with specific ERES, whereas transmembrane secretory proteins distribute throughout the ER membrane.

This discovery represents a major advance in understanding how proteins are distributed in cells to perform their vital functions, and could open the door to understanding the causes of diseases associated with failures in protein distribution at the cellular level: from cancer to neurodegenerative diseases, such as Alzheimer’s.

The study was carried out by the Department of Cell Biology’s Membrane Trafficking research group, part of the Faculty of Biology of the University of Seville and the IBiS, led by Professor Manuel Muñiz Guinea, in collaboration with the universities of Hiroshima (Japan), Geneva and Fribourg (Switzerland). The RIKEN Institute in Japan, where the “Super-resolution Living Cell Microscopy” Laboratory is located, also participated in this project. This is a unique facility in the world which conducted analyses using a high resolution fluorescence microscope that allows the study of very fast and dynamic processes in living cells on an incredibly small scale.

The proteins are manufactured in a compartment of the cell and then have to be distributed correctly by exiting through specific “doors.” In this study, scientists from Seville discovered that membrane lipids are responsible for selecting and directing certain proteins to the correct exit doors.

To make this discovery, they designed a “mutant cell” that was programmed to manufacture a shortened version of cellular lipids called ceramides. The researchers suspected that the length of these lipids could be a determining factor in choosing the appropriate exit door.

And that’s exactly what we found. Thanks to the short ceramides we generated, we were able to demonstrate for the first time that lipids are only able to guide proteins during transport if they are the right length. Moreover, by using such a powerful ‘super microscope’ we were able to capture for the first time on an ultra small scale andin vivohow proteins exit through these molecular doors.

As a curiosity, this study was carried out using yeast cells (the same unicellular fungus used to make bread, beer and wine) as a model organism, because, being eukaryotic cells just like ours, they perform the same basic cellular processes in a very similar way, so the observations can be extrapolated to human cells.

In conclusion,the article published in Science Advances has also served to demonstrate that lipids and proteins influence each other to self-organize together within the cell, and points out that the mechanism they have discovered and used for this could be used in other processes, such as the entry and exit of certain viruses from the cell, as well as in the formation of exosomes (extra-cellular lipid vesicles involved in communication between cells, particularly in cancer).

Chain length of ceramide in the endoplasmic reticulum membrane is critical for sorting selectivity - Medicine Innovates
Fig. 1 Newly synthesized C26 ceramide–based GPI-AP cargos form clusters in the ER membrane adjacent to specific ERES.Science Advances (2020). DOI: 10.1126/sciadv.aba8237

About the author

Howard Riezman received a Bachelors of Arts degree (1975) from Washington University in Saint Louis where he began his research career working on the lac operon from E. coli. He then moved to the University of Wisconsin-Madison under the supervision of Wayne M. Becker where he completed his PhD in Botany (1980) working on the biogenesis of glyoxysomal enzymes. He crossed the Atlantic to work as a postdoctoral fellow (Jane Coffin Childs Fellow) with Gottfried (Jeff) Schatz as a mentor on the biogenesis of mitochondria at the Biozentrum of the University of Basel.

In 1983 he started his independent laboratory at the ISREC in Lausanne initiating studies on the endocytic pathway in yeast. He moved back to the Biozentrum as Full Professor (1988) where he continued his work on endocytosis and began studying GPI-anchored protein biosynthesis and traffic. In 2002 he moved to the Biochemistry department of the University of Geneva. He continues working on membrane trafficking, but has changed the emphasis of his research to the understanding of the metabolism and function of membrane lipids.

Howard Riezman was elected member of EMBO in 1997 and has served as department chairman in both Basel and Geneva. He has served on the Research Council of the Swiss National Science Foundation (SNSF) for 8 years and is currently a member of the Foundation Council of the SNSF. His work has received generous funding from the SNSF since 1983, as well as from the HFSPO, EU and ESF. He has recently been awarded the directorship of a National Center for Competence in Research (NCCR) in Chemical Biology by the Federal Department of the Interior.

Reference

Sofia Rodriguez-Gallardo, Kazuo Kurokawa, Susana Sabido-Bozo, Alejandro Cortes-Gomez, Atsuko Ikeda, Valeria Zoni, Auxiliadora Aguilera-Romero, Ana Maria Perez-Linero, Sergio Lopez, Miho Waga, Misako Araki, Miyako Nakano, Howard Riezman, Kouichi Funato, Stefano Vanni, Akihiko Nakano, Manuel Muñiz. Ceramide chain length-dependent protein sorting into selective endoplasmic reticulum exit sites. Science Advances  11 Dec 2020: Vol. 6, no. 50, eaba8237, DOI: 10.1126/sciadv.aba8237

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