How nutrient-starved cells recycle internal components

Date:
July 16, 2020
Source:
Harvard Medical School
Summary:
Researchers systematically surveyed the entire protein landscape
of normal and nutrient-deprived cells to identify which proteins
and organelles are degraded by autophagy.



FULL STORY ==========================================================================
The idea of the cell as a city is a common introduction to biology,
conjuring depictions of the cell's organelles as power plants, factories, roads, libraries, warehouses and more. Like a city, these structures
require a great deal of resources to build and operate, and when resources
are scarce, internal components must be recycled to provide essential
building blocks, particularly amino acids, to sustain vital functions.


==========================================================================
But how do cells decide what to recycle when they are starving? One
prevailing hypothesis suggests that starving cells prefer to recycle
ribosomes -- cellular protein-production factories rich in important
amino acids and nucleotides - - through autophagy, a process that degrades proteins in bulk.

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

The analyses revealed that, in contrast to expectations, ribosomes are
not preferentially recycled through autophagy, but rather 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
on autophagy and protein degradation processes, which are increasingly
popular targets for drug development in cancers and other disease
conditions, the authors said.

"When cells are starving, they don't haphazardly degrade ribosomes
en masse through autophagy. Instead, they appear to have mechanisms
to control what they recycle," said senior study author Wade Harper,
the Bert and Natalie Vallee Professor of Molecular Pathology and chair
of cell biology in the Blavatnik Institute at HMS.



==========================================================================
"Our findings now allow us to rethink previous assumptions and better understand how cells deal with limited nutrients, a fundamental question
in biology," Harper said.

Protein turnover is a constant and universal occurrence inside every
cell. To recycle unneeded or misfolded proteins, remove damaged
organelles, and carry out other internal housekeeping tasks, cells
utilize two primary tools, autophagy and the ubiquitin-proteasome system.

Autophagy, derived from Greek words meaning "self-eating," allows cells
to degrade proteins in bulk, as well as larger cellular structures,
by engulfing them in bubble-like structures and transporting them to
the cell's waste disposal organelle, called the lysosome.

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

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



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

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

"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,"
Harper said. "This simple result hides a huge amount of biology that we
tried to uncover." Searching for an explanation for this discrepancy,
the team, spearheaded by study co-first authors Heeseon An and Alban
Ordureau, research fellows in cell biology at HMS, systematically
analyzed the production of new ribosomes and the fate of existing ones
in starving cells.

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

When cells were deprived of nutrients, the primary factors that led to
lower overall ribosome levels was a reduction in new ribosome synthesis
and turnover through non-autophagy dependent pathways, the experiments
showed. Both cell volume and the rate of cell division decreased as well, however, which allowed cells to maintain a cellular density of ribosomes.

Global picture Next, the team examined the patterns of degradation
for more than 8,300 proteins throughout the cell during nutrient
deprivation. They confirmed that the pattern of ribosome turnover appeared
to be independent of autophagy and, instead, matched proteins that are
known to be degraded via the ubiquitin- proteasome system.

"With our quantitative proteomics toolbox, we could look simultaneously
in an unbiased manner at how thousands of proteins are made and turnover
in the cell under different conditions with or without autophagy,"
Ordureau said. "This allowed us to gain a global picture that wasn't
based on inferences drawn from analyses of a limited number of proteins."
The analyses showed that a small number of organelles and proteins were degraded by autophagy in higher amounts than ribosomes, particularly endoplasmic reticulum, which the Harper lab has previously shown is
selectively remodeled by autophagy during nutrient stress.

These proteome-wide data may reveal other organelles and proteins that
are selectively degraded in response to nutrient stress, the authors said,
and the team is pursuing further analyses.

Together, the findings shed light on how starving cells respond to
nutrient stress and, in particular, clarify previous assumptions regarding ribosome turnover. Critically, the authors said, the results demonstrate
that proteasome-dependent turnover of ribosomes likely contributes to
a much greater extent than autophagy during nutrient 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.

"Controlling autophagy is being explored in a wide range of contexts
such as killing tumor cells by starving them of key nutrients or
allowing neurons to remove harmful protein aggregates," An said. "But
our understanding of autophagy is incomplete, and many aspects are
still unclear." Only relatively recently have scientists found that starvation-induced autophagy can be selective, she added, and questions
such as what organelles are targeted and why, whether autophagy affects
only damaged organelles or random ones, and many others remain mostly unanswered.

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

Additional authors on the study include Maria Ko"rner and Joao
Paulo. The work was supported by the National Institutes of Health
(grants R37NS083524, RO1AG011085 and RO1GM095567).


========================================================================== Story Source: Materials provided by Harvard_Medical_School. Original
written by Kevin Jiang.

Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Heeseon An, Alban Ordureau, Maria Ko"rner, Joao A. Paulo, J. Wade
Harper.

Systematic quantitative analysis of ribosome inventory
during nutrient stress. Nature, 2020; 583 (7815): 303 DOI:
10.1038/s41586-020-2446-y ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/07/200716123008.htm

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