A look into the heart of cellular waste disposal

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Researchers make visible how a nanomachine takes care of cleaning up in the cell

Fluorescent lipids reveal how the nanomachine accelerates lipid transfer on dema
Fluorescent lipids reveal how the nanomachine accelerates lipid transfer on demand. © MPI f. Multidisciplinary Natural Sciences & Pouya Hosnani / University Medical Center Göttingen/ Anh Nguyen

To keep our body’s cells from overflowing with waste and to keep them healthy, the waste inside them is constantly being disposed of. This cleaning process is called autophagy. Scientists have now, for the first time, recreated in the laboratory the complex nanomachine that starts this process and found that it works quite differently from other cellular machines. The researchers’ new insights could open up new approaches for the treatment of cancer, immune disorders and neurodegenerative diseases, and possibly even delay aging.

Once again the house cleaning postponed, the basement room overflowing with bulky waste? Living cells cannot afford this procrastination when it comes to clearing the decks. Tiny garbage chutes are constantly active there to get rid of discarded proteins, faulty cell components or defective organelles. These garbage chutes, called autophagosomes, fish out the discarded components before they accumulate in the cell and cause damage. The cellular garbage is then passed on to the cell’s own recycling machinery, the lysosome, where it is digested and recycled. Thus, the cell quickly has building blocks available again for new cellular components. The autophagy process, literally self-eating, thus also contributes to cells surviving stress or periods of starvation.

However, autophagy also serves another important purpose. It renders harmless viruses and bacteria that successfully bypass the immune system’s defenses and reach the cell plasma. The consequences are correspondingly fatal if the autophagy process is faulty, too slow or too fast. Neurodegenerative diseases and cancer can develop or disorders of the immune system can occur. Aging processes also seem to accelerate.

Autophagy is a highly complex process involving many different proteins and protein complexes. We know many of them, but there are still fundamental gaps in our knowledge," reports Alex Faesen , research group leader at the Max Planck Institute for Multidisciplinary Natural Sciences in Göttingen. "How do the protein components work together? How is the process of autophagy started and stopped? When and where is the autophagosome assembled? That’s what we want to find out."

Nanomachine at work

His team has now succeeded for the first time in producing all the proteins involved in the autophagy process in the laboratory and observing them directly during the assembly of the autophagosomes. This was a mammoth project lasting several years for the entire research group, which cooperated with the teams led by Björn Stork from the University of Düsseldorf and Michael Meinecke, formerly at the University Medical Center Göttingen, now at the Heidelberg University Biochemistry Center. There were many challenges," Faesen reports. In the first step, the researchers produced each individual protein component in the laboratory. The standard approach is to use bacteria that are genetically reprogrammed to produce the desired protein in large quantities. But protein production with bacteria did not work for any of our proteins," says the Göttingen biochemist. Instead, the researchers switched to insect cells as molecular helpers - the breakthrough.

In the next step, the team brought the individual protein complexes together. The complexes self-assembled into a protein supercomplex, the autophagy initiation complex. In fact, a sophisticated cellular nanomachine is at work in autophagy - and it works quite differently than previously thought," says the group leader.

To produce autophagosomes, the autophagy initiation complex first creates a junction between a specific structure of the cell, the endoplasmic reticulum, and the autophagosome that is being formed. Under stress or in times of starvation, such as during endurance sports, this occurs within just a few minutes. "From this point on, there is no turning back: the garbage chute is assembled and collects the cellular waste," explains Anh Nguyen, one of the two first authors of the study. Co-first author Francesca Lugarini adds, "Via the contact site, fat-like molecules called lipids are transported to a precursor stage of the autophagosomes and incorporated there." These grow and thereby enclose the cell material to be degraded - the finished mini-organelle is formed. Within just 20 minutes of its formation, the autophagosome already delivers its waste to the lysosome by fusing with it.

Protein origami for "on" and "off".

But what starts the assembly of the autophagy machine, what starts it and what stops it? The researchers did not find a molecular "on" and "off" switch as in other molecular machines. Instead, it is started and stopped by means of "protein origami". Certain molecules, called ATG13 and ATG101, change their shape for this purpose. This affects how they bind to other proteins in the nanomachine. This protein transformation also triggers the assembly of the autophagy initiation complex at the right time and in the right place," says Faesen, describing the special features of the nanomachine.

The team hopes that the new findings will advance the development of future drugs that can be used to treat diseases caused by a defective autophagy process.

Nguyen A, Lugarini F, David C, Hosnani P, Alagöz Ç, Friedrich A, Schlütermann D, Knotkova B, Patel A, Parfentev I, Urlaub H, Meinecke M, Stork B, Faesen AC.