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Autophagy - recycling and survival

Cells are highly economical and environmentally conscious. Components that are no longer needed are degraded and returned to the cellular metabolism. This tightly regulated catalytic process is a major survival mechanism used by starving cells to reallocate nutrients to essential processes. Dr. Jörn Dengjel and his team from the Freiburg Institute for Advanced Studies (FRIAS) are aiming to decipher the molecular and cell biological mechanisms of this recycling process, which is also known as autophagy or autophagocytosis. Detailed insights into these mechanisms will also help to improve the researchers’ understanding of diseases such as cancer and Alzheimer’s. Dengjel and his team starve their cells and closely monitor the cells’ molecular responses.

Humans have only learned to build recycling plants over the last decades. Biological cells, however, have been proficient in using the principle of waste disposal and recycling for billions of years. Cell biologists know two degradation pathways that cells use to return defective or no longer needed cell components into the metabolism.

One of these pathways involves proteasomes and the other, autophagosomes. Large protein complexes inside eukaryotes, known as proteasomes, degrade smaller debris such as peptides and proteins. The process of autophagy or autophagocytosis involves the degradation of larger structures such as protein complexes or organelles such as mitochondria and ribosomes. Autophagocytosis not only removes cellular waste originating from erroneous production, UV irradiation or heat. It is a so-called constitutive catalytic process, which means that it is constantly active at a low level. However, in times of nutrient starvation, the autophagy machinery operates at full speed. In principle, the cells break down parts of themselves in order to ensure that vital processes can continue. “We make use of this situation in order to investigate the molecular mechanisms underlying the process of autophagy,” said Dr. Jörn Dengjel, head of the Protein Dynamics Group at the Center for Biological Systems Analysis (ZBSA) in Freiburg.

What role does autophagy play in Alzheimer’s and cancer?

Cell biologists understand the recycling processes very well on the morphological level. Organelles and protein complexes are broken down inside the cell in a so-called autophagosome. This is a vesicle surrounded by two membranes. During the autophagic process, the autophagosomes fuse with a lysosome that contains the enzymes required to degrade the contents into their molecular constituents. But how does a cell know which structures need be degraded? How exactly do the autophagosomes develop? And which molecules mediate and control the entire process?

Two photos with green cells and blue nuclei. The photo on the left shows the nuclei located in a green cloud; in the photo on the right, the green colour is restricted to grains and the nuclei are no longer surrounded by green spots.
These breast cancer cells were labelled with a fluorescence-labelled autophagosome marker (eGFP-LC3; green). When left untreated, the cytoplasm is diffusely stained. (A). The cells were subsequently starved for 24 hours (no amino acids and no serum). The photo shows an accumulation of green spots, which represent the autophagosomes (B). The cell nuclei are stained blue. Size scale: 10 µm.   © Dr. Jörn Dengjel

All these questions are also of medical relevance since autophagy plays an important role in many diseases. For example, protein aggregations (known as plaques) deposited in the brain of Alzheimer’s patients develop due to defective autophagic processes, amongst other things. The recycling of cellular components also plays an important role in cancer cells, in a twofold sense: cells in the outer areas of a tumour need to block the process in order to avoid being degraded (autophagy can also be lethal and is referred to as type II cell death, apoptosis is known as type I cell death). Cells located in the centre of a tumour are cut off from the nutrient supply and need to partially degrade themselves in order to survive. Can researchers find molecular autophagy controllers in cancer cells that can be targeted with medicines?

Any type of starvation has its specific consequences

The researchers from Freiburg use a mass spectrometer to scan the proteome of cells. © FRIAS

Dengjel and his team pursue a systemic approach. They are looking for proteins and signalling molecules that play a particular role when cells increase their autophagosomal activity. They use mass spectrometry to scan the entire range of proteins formed in a cell, i.e. the proteome. They compare cells that “digest themselves” under normal conditions with cells with a higher autophagosomal activity. To carry out such comparisons, they need to starve the cells by reducing the supply of amino acids, for example. “If starving cells produce particularly high quantities of certain proteins, it is a possible indication of the important role they play in the autophagic process,” said Dengjel. Another approach focuses on identifying proteins that are equipped with phosphate groups when the cells are deprived of nutrients. It is assumed that such proteins play a key role in autophagy-related signalling as their phosphate groups are transferred from one signalling molecule to another in cellular signalling cascades, thereby leading to the activation of subsequent signalling steps.

Biologists have long regarded autophagy as an unspecific process. They have assumed that an autophagosome devours anything it comes into contact with. However, Dengjel and his team have been able to show that this is not the case. After 36 hours of amino acid deprivation, the researchers from Freiburg found that not all proteins and cellular constituents are broken down equally quickly. Ribosomes and molecules that are required for protein biosynthesis are the first cellular components that are broken down. This is because the cell does not need them due to the fact that amino acids are not available for protein synthesis.

Molecular background and systems work

Is there a lack of amino acids? Lipids? Carbohydrates? Or does the cell need to get rid of defective components arising from damage caused by chemicals? The composition of a cell’s proteome changes in relation to these “stimuli”. “We can virtually exclude the possibility of autophagy being an unspecific process,” said Dengjel who actually believes that it is highly specific. The work of other researchers shows that any type of organelle undergoes a specific autophagic process: mitophagy is selective for the degradation of mitochondria; reticulophagy is selective for the endoplasmic reticulum and ribophagy is selective for ribosomes. Using proteomics methods, Dengjel and his team are aiming to identify the molecules that mediate and control these specific processes. They have already identified some candidates. These proteins are produced in higher quantities following a specific hunger stimulus after which they also appear in the autophagosomes. The biologists from Freiburg are now investigating the molecular function of these proteins.

Research group led by Dr. Jörn Dengjel (4th from the right) from the Freiburg Institute for Advanced Studies (FRIAS). © Dr. Jörn Dengjel

The eight people that work in Dengjel’s laboratory all focus on projects related to autophagy and investigations into the molecular basis of certain genetic skin diseases, disorders in which defects of the endoplasmic reticulum play a role. Defective endoplasmic reticulums are degraded by the process of autophagy. In their work which is linked to a clinical research project, Dengjel and his team work closely with researchers from the Department of Dermatology at the Freiburg University Medical Centre. “Interdisciplinary cooperation is very important for us,” said Dengjel highlighting that cooperative projects with research groups from Switzerland, the USA, Denmark or Israel and the close cooperation with bioinformaticians, mathematicians and physicians from the ZBSA and the University of Freiburg is actually indispensable for the systems biology approach Dengjel and his team are using.

All empirical experiments need to be backed with theoretical models. Statistical methods need to be used to manage the huge amount of data produced. Computer simulations can lead to a better understanding of the processes investigated and lead to new hypotheses. “The basic research relating to autophagy is just starting out,” said Dengjel going on to add “but one day we might potentially be able to contribute to improving the treatment of diseases such as Alzheimer’s and cancer.”

Further information:

Dr. Jörn Dengjel
University of Freiburg
Albertstr. 19
79104 Freiburg
Tel.: 0049-(0)761/203-97208
E-mail: joern.dengjel(at)frias.uni-freiburg.de

Website address: https://www.gesundheitsindustrie-bw.de/en/article/news/autophagy-recycling-and-survival