Same same, but different

Molecular structure of the Rag dimers.

Evolution made nutrient sensing more precise in mammalian cells

Our cells use nutrients from their environment to grow and proliferate. To properly respond to fluctuating nutrient levels, our cells possess delicate molecular mechanisms that ‘read’ and ‘transmit’ information about the overall nutrient status. At the core of this machinery lies the mTOR kinase and the so-called Rag GTPases that control mTOR localization in cells. Although human cells contain four distinct paralogous Rag genes, the four different Rag dimers that can be formed by the respective proteins were assumed to be functionally identical. Now, a new study by the Demetriades group at the Max Planck Institute for Biology of Ageing shows that this is not the case, and suggests that mammalian cells have developed ways to regulate the activity of mTOR more precisely than previously thought.

Cells need to be able to sense if nutrients are available in their environment, so that they only grow when they have everything they need. The most important nutrient sensor in cells is a protein called mTOR, whose activity is tightly controlled by a large number of regulatory proteins. Proper function of this machinery is crucial for human health, whereas its dysregulation is tightly linked to life-threatening diseases and ageing in humans. "Understanding the intricate details of how this works in cells is fundamental to knowing how and why we age", explains Constantinos Demetriades, research group leader at the Max Planck Institute for Biology of Ageing, who led the study.

All Rags are equal?

When nutrients—in particular amino acids—are abundant, mTOR is activated on the surface of lysosomes - special organelles in the cell, where it is anchored by a set of proteins called Rag GTPases (or Rags, in short). While lower organisms like yeast or flies have only two Rag proteins that form a single complex, mammalian cells express four different Rags (RagA-D) that can combine to form four distinct complexes. Because the different Rags are very similar to each other, until now, researchers considered them functionally equivalent and used them interchangeably in experiments to study how mTOR is regulated by nutrients. “Knowing how evolution works, this did not make much sense”, Demetriades says. “When genes are duplicated, and the new copies remain active, this is usually because they acquire a slightly different function, compared to the ancestral ones, to help cells function more precisely”. Driven by this and by previous experimental observations, the MPI scientists decided to challenge the idea that all Rags are made equal.

Functionally different Rag complexes

To test their hypothesis, they first modified cultured human cells in a way that all four Rag genes are switched off, and then re-inserted one Rag dimer pair at a time. Using these different cell lines, they found that the different Rag complexes were indeed functionally divergent: The presence of one particular Rag protein (RagD) determined which mTOR targets are being activated, while another Rag (RagB) interfered with the ability of mTOR to respond to depletion of amino acids, thus making cells partially insensitive to starvation (1).

Fine-tuning the mTOR signalling pathway

Based on their findings, the researchers propose that these additional Rag complexes are there to help mammalian cells fine-tune the activity of the mTOR signaling pathway in a more precise manner. For example, RagB-containing complexes may help cells to maintain some mTOR activity even when nutrient levels are low, to sustain functions crucial for their response to starvation. Because different cell types express Rag proteins at different ratios, an alternative scenario is that the presence of two additional Rags in mammalian cells specifies how certain tissues respond to low nutrients. The latter hypothesis is also supported by an accompanying study from another group in DKFZ, Heidelberg, who suggested RagB may play a special role in brain cells.

“Our study highlights the complexity of the cellular nutrient sensing machinery in mammals. Only when we understand the fine details of how this actually works, and what goes wrong when we get sick or when we age, we will be able to suggest improved and more specific ways to tackle these mTOR-related conditions more effectively”, Demetriades comments.

Original Publication:

Peter Gollwitzer, Nina Grützmacher, Sabine Wilhelm, Daniel Kümmel, Constantinos Demetriades
A Rag GTPase dimer code defines the regulation of mTORC1 by amino acids.
Nat. Cell Biol., Sep 2022

Learn more about the work in the Demetriades group.