Autophagy and the Fight Against Viruses

HIV: trace leads into the recycling system of the cell

The live dose shows how the HIV protein Nef (red) and the autophagy protein GABARAP (green) are secreted together (excreted) from the cell. Copyright: Forschungszentrum Jülich

On December 10th, this year’s Nobel Prize in Medicine will be awarded in Stockholm for research into the molecular basis of autophagy. As recent research has shown, this “recycling system” of the cell is associated with numerous diseases-relevant processes in the organism. An important example of this are viral infections. Scientists at the Jülich Institute of Complex Systems (ICS-6) have identified a human immunodeficiency virus (HIV) protein, which seems to be a part of the autophagy system High-end methods should be pursued further. Postdoc and working group member Dr. Alexandra Boeske gives an insight into the research and explains the decisive advantages of the combination of structural and cell biology.

Dr. Boeske, the international World AIDS Day on December 1, recalled that there are still no real cures for over 36 million people infected with HIV worldwide. They are investigating a link between HIV and the autophagy system in the cell in Jülich. What is the relationship?

We are investigating a very specific interaction between components of the autophagy system and HI virus, which might explain an unexplained step in the infection. This is mainly about HIV-Nef, one of only 17 proteins of the virus. It comes directly with the virus particles into the cell, is additionally produced after the infection in masses and is considered decisive for the fact that in the course of the infection an immune weakness, ie AIDS, develops. It is important that Nef does not only have a destructive effect in the infected cell, but also reaches the outside where it triggers a kind of self-destructing program in healthy neighboring cells, the so-called apoptosis. So far it is not clear how the protein succeeds to get out of the cell – the classical path of secretion can not use it. We suspect that it is doing some sort of “highjacking” of parts of the autophagy system to be transported outside.

How can you imagine this “autophagy system”?

During autophagy, small membran-coated vesicles, so-called vesicles, are formed in the plasma of the cell, which, for example, enclose non-required cell components.They then fuse with another vesicle type, the lysosomes, which contain enzymes, from which the contents are decomposed into small building blocks. These are then available to the cell again. The process is based on a complex structure of special protein molecules called ATGs. Yoshinori Ohsumi described the first 15 of them in the nineties, which is the pioneering achievement for which he receives the Nobel Prize this month. His discoveries have led to today’s autophagy research. Although the studies were conducted on yeast cells, the process is so fundamental that it finds itself in a similar way in all eukaryotic organisms. Since then, further ATGs have been discovered and understand that autophagy is much more than just a recycling system. As a defense against infectious diseases, for example, it can remove foreign bodies such as viruses and bacteria. However, some pathogens have learned to escape autophagy or in some cases even to manipulate and use it for themselves.

And HIV would be such a case?

Precisely – in the case of the infected cells, the autophagy machinery is activated, but the fusion with the lysosomes no longer takes place. Thus the vesicle vesicles accumulate in the interior of the cell and finally reach the outside. In some of these vesicles, we find HIV-Nef together with a certain type of human ATG proteins called GABARAP. We have found that a lack of these GABARAP proteins in cultured human cells means that Nef can no longer be transported outside. We combine such cell biologic observations with structural biology to understand the mechanism. At the biomolecular NMR center in Jülich, for example, the 3D structures of the human GABARAP proteins could be decoded and the binding site for HIV-Nef identified on the molecular surface.

Could this interaction with a drug be blocked as a treatment approach?

Somehow, perhaps, if what we observe in the cell culture system also happens in the patient. Finally, Nef must be able to leave his cell of origin, in order to be able to drive his illness also in cells not primarily affected by the infection. But at the moment we do not think of something like that yet. We simply do not know enough.

What are the next plans?

We must first understand what is really going on in the cell and work on a model that shows step by step what HIV Nef does to get outwards – including all possible intermediate steps. This sounds like a relatively small question, but in practice this is very complex. We, the working group of Dr. Silke Hoffmann, in which I am working, the group of Dr. Melanie Schwarten and Prof. Dieter Willbold, have received funds from the German Research Foundation within the framework of a special research area and have now been able to build up a strong team. In the near future, we will now use a whole series of new methods, such as cryo-electron microscopy to view the exact nature of the vesicles, or the gene editing method CRISPR to identify other factors important for the secretion of Nef. In addition, we will elucidate further structures with NMR spectroscopy, including the complex resulting from the combination of the two proteins. In the end, we hopefully know exactly what mechanisms are being used to transfer HIV-Nef from the cell.

Is this so often the case in virology that structural and cell biology is so closely linked?

No, this is even very rare. Frequently, some make their cell experiments and perhaps find an interesting interaction. Very different working groups then determine the structures of the molecules involved. The specialization is quite big. I also notice this at conferences, as it is often astonished that we combine structural and cell biology directly from the beginning in Jülich.

And is that an advantage?

In any case. I have been working on this topic in Jülich since six years, since my diploma thesis, and I think you learn more through this work. Ultimately, what we see in the cell is based on the structural interactions of the molecules. The biological relevance of the structures is to be understood only in the context of their function in the cell. So you learn a lot from one discipline for the other.