New study sheds light on how nutrient-deprived cells recycle internal components

The idea of ​​the cell as a city is a common introduction to biology, evoking representations of the cell’s organelles such as power plants, factories, roads, libraries, warehouses, and more. Like a city, these structures require a large amount of resources to build and operate, and when resources are scarce, the internal components must be recycled to provide essential building blocks, particularly amino acids, to maintain vital functions.

But how do cells decide what to recycle when they starve? A prevailing hypothesis suggests that starving cells prefer to recycle ribosomes, factories for the production of cellular proteins rich in amino acids and important nucleotides, through autophagy, a process that breaks down proteins en masse.

However, new research by scientists at Harvard Medical School suggests otherwise. In a study published in Nature in July, they systematically examined the entire protein landscape of normal, nutrient-deprived cells to identify which proteins and organelles are degraded by autophagy.

Analysis revealed that, in contrast to expectations, ribosomes are not preferentially recycled by autophagy, but a small number of other organelles, particularly parts of the endoplasmic reticulum, are degraded.

The results shed light on how cells respond to nutrient deprivation and autophagy and protein degradation processes, which are increasingly popular targets for drug development in cancers and other diseases, the authors said.

“When cells starve, they don’t accidentally break down mass ribosomes through autophagy. Instead, they appear to have mechanisms to control what they recycle,” said study lead author Wade Harper, professor of molecular pathology at Bert and Natalie. of cell biology at the Blavatnik Institute at HMS.

“Our findings now allow us to rethink past assumptions and better understand how cells handle limited nutrients, a fundamental question in biology,” said Harper.

Protein turnover is a constant and universal occurrence within every cell. To recycle unnecessary or misfolded proteins, remove damaged organelles, and perform other internal cleaning tasks, cells use two main tools, autophagy and the ubiquitin-proteasome system.

Autophagy, derived from the Greek words for “self-eating,” allows cells to break down bulk proteins as well as larger cell structures, wrapping them in bubble-like structures and transporting them to the cell’s waste-removing organelle. , called a lysosome.

Rather, the proteasome pathway allows cells to break down individual proteins by labeling them with a marker known as ubiquitin. Ubiquitin-modified proteins are recognized by the proteasome and degraded.

Surprising discrepancy

Previous studies in yeast have suggested that nutrient-deprived cells use autophagy to specifically recycle ribosomes, which are abundant and a reservoir of key nucleotides and amino acids. However, cells have many other mechanisms to regulate ribosome levels, and how they do this when nutrients are low is not fully understood.

Using a combination of quantitative proteomics and genetic tools, Harper and his colleagues investigated protein composition and turnover in cells that were deprived of key nutrients. To test the role of autophagy, they also focused on cells with genetically or chemically inhibited autophagy systems.

One of the first analyzes they carried out revealed that, in hungry cells, total ribosomal protein levels decrease only slightly relative to other protein levels. This reduction appeared to be independent of autophagy. Cells that lacked autophagy had no obvious defects when they lacked nutrients.

“This was a very surprising finding that was at odds with existing hypotheses, and it really led us to consider that something was missing in how we think about autophagy and its role in ribosome degradation,” said Harper. “This simple result hides a lot of biology that we are trying to discover.”

In search of an explanation for this discrepancy, the team, led by the study’s first authors, Heeseon An and Alban Ordureau, researchers in cell biology at HMS, systematically analyzed the production of new ribosomes and the fate of existing ones in cells. hungry.

They did this through a variety of complementary techniques, including Ribo-Halo, which allowed them to label different ribosomal components with fluorescent labels. They could apply these labels at different time points and measure how many new ribosomes were synthesized at the single cell level, as well as how many old ribosomes remained after a set period of time.

When cells were deprived of nutrients, the main factors that led to the decrease in overall ribosome levels was a reduction in new ribosome synthesis and renewal through non-autophagy-dependent pathways, the experiments showed. However, both cell volume and cell division rate also decreased, allowing cells to maintain a ribosome cell density.

Global picture

The team then examined the degradation patterns of more than 8,300 proteins throughout the cell during nutrient deprivation. They confirmed that the renewal pattern of ribosomes appeared to be independent of autophagy and, instead, paired proteins known to be degraded through the ubiquitin-proteasome system.

“With our quantitative proteomics toolkit, we could simultaneously impartially observe how thousands of proteins are produced and turnover in the cell under different conditions with or without autophagy,” Ordureau said. “This allowed us to obtain a global image that was not based on inferences drawn from analyzes of a limited number of proteins.”

Analysis showed that a small number of organelles and proteins were degraded by autophagy in greater amounts than ribosomes, particularly the endoplasmic reticulum, which Harper’s laboratory has previously shown to be selectively remodeled by autophagy during nutritional stress.

These proteome-wide data may reveal other organelles and proteins that are selectively degraded in response to nutritional stress, the authors said, and the team is conducting additional analyzes.

Together, the findings shed light on how hungry cells respond to nutritional stress, and in particular shed light on previous assumptions about ribosome turnover. Critically, the authors said, the results demonstrate that proteasome-dependent ribosome turnover probably contributes much more than autophagy during nutritional stress.

This is an important step toward a better unbiased understanding of autophagy, a widely studied process that is the target of numerous drug discovery efforts.

“Autophagy control is being explored in a wide range of contexts, such as killing tumor cells by depriving them of key nutrients or allowing neurons to kill harmful protein aggregates,” An said. “But our understanding of autophagy is incomplete and many aspects are still unclear. “

Scientists recently discovered that hunger-induced autophagy can be selective, he added, and questions like which organelles are targeted and why, if autophagy only affects damaged or random organelles, and many others remain largely unanswered.

“We are using the context of starvation to better understand how cells use autophagy, and under what circumstances, to better understand this important process,” An said.