Scientists have discovered a new way for cells to break down proteins they don’t need, which affect genes important for nerve, immunity and development. This discovery might lead to a treatment for conditions caused by an imbalance of proteins in cells.
This mechanism breaks down short-lived proteins that support brain and immune function
Short-lived proteins control gene expression in cells and perform important roles ranging from aiding brain communication to enhancing the body’s immune response. These proteins originate from the nucleus, and rapidly degrade once they have served their purpose.
For decades, the mechanisms behind the breakdown of these important proteins and their removal from cells have remained a mystery to researchers to this day.
In an interdepartmental collaboration, researchers from Harvard Medical School have identified a protein called medullinulin that plays a critical role in the degradation of many short-lived nuclear proteins. Studies show that meduline does this by taking proteins directly and dragging them into the cellular waste system, called the proteasome, where they are broken down.
The results were recently published in the journal Science.
“These short-lived proteins have been known for more than 40 years, but no one knows exactly how they are degraded,” said co-lead author Shen Guo, a research neurobiology at HMS.
Because the proteins broken down by this process modulate genes with important functions related to the brain, immune system, and development, scientists may eventually target the process as a way to control protein levels to alter these functions and correct any malfunctions.
“The mechanism we found is very simple and elegant,” added lead author Christopher Nardoni, PhD candidate in genetics at HMS. “This is a fundamental scientific discovery, but there are many implications for the future.”
The molecular puzzle
It is known that cells can break down proteins by binding to small molecules called ubiquitin. The tag tells the proteasome that the protein is no longer needed and destroys it. Much of the pioneering research into this process was carried out by the late Fred Goldberg at HMS.
However, sometimes the proteasome breaks down proteins without the aid of ubiquitin tags, leading researchers to suspect other mechanisms of proteolysis that are independent of ubiquitin.
“There is a lot of evidence in the scientific literature that the proteasome can directly degrade unsigned proteins, but no one really understands how that happens,” says Nardoni.
One group of proteins that appears to be degraded by alternative mechanisms are stimulus-induced transcription factors: proteins synthesized rapidly in response to cellular stimuli that travel to the cell nucleus to turn on genes, which are then rapidly destroyed.
“What first surprised me is that these proteins are very unstable and have very short half-lives – once produced, they do their job, and very quickly after that they degrade,” says Joe.
This transcription factor supports many important biological processes in the body, but even after decades of research, “the mechanisms for its conversion remain largely unknown,” said Michael Greenberg, the Nathan March Posey Professor of Neurobiology at HMS Blavatnik Institute and Harvard. University. . Co-author of this paper with Stephen Eledge, Gregor Mendel Professor of Genetics and Medicine at HMS and Brigham and Women’s Hospital.
From a few to hundreds
To investigate this mechanism, the team started with two familiar transcription factors: Fos, which has been studied extensively in the Greenberg lab for its role in learning and memory, and EGR1, which is involved in cell division and survival. Using state-of-the-art proteomics and genetic analysis developed in Elledge’s lab, the researchers focused on meduline as a protein that helps break down transcription factors. Follow-up experiments revealed that apart from Fos and EGR1, meduline may also be involved in the degradation of hundreds of other transcription factors in the nucleus.
Gu and Nardone remembered how shocked and skeptical they were of their findings. To confirm their findings, they decided they needed to know exactly how meduline targets and degrades many different proteins.
“Once we identified all these proteins, there were a lot of tantalizing questions about how the medullinolenic mechanism actually works,” says Nardoni.
With the help of a machine learning tool called AlphaFold that predicts protein structure, as well as the results of a series of laboratory experiments, the team was able to explain the details of the mechanism. They showed that the meduline has a ‘capture domain’ – a region of the protein that captures other proteins and channels them directly into the proteasome, where they are cleaved. This capture domain consists of two separate regions connected by amino acids (think a glove with strings) that capture a relatively unstructured region of a protein, allowing medullin to capture a wide variety of protein types.
Of note are proteins such as Fos which are responsible for activating genes that trigger neurons in the brain to connect and reconnect themselves in response to stimuli. Other proteins such as IRF4 activate genes that support the immune system by ensuring that cells are able to form functioning B and T cells.
“The most exciting aspect of this research is that we now understand a new general mechanism independent of ubiquitylation that degrades proteins,” said Elledge.
The tantalizing potential of translation
In the short term, the researchers want to dig deeper into the mechanism they discovered. They plan to carry out structural studies to better understand the details of how proteins are captured and degraded. They also worked with mice, deficient in linulin, to understand the role of the protein in different cells and developmental stages.
Scientists say their findings have tantalizing potential for translation. This may provide a pathway that researchers can exploit to control transcription factor levels, thereby modulating gene expression and, in turn, related processes in the body.
“Protein degradation is an important process, and its deregulation underlies many disorders and diseases,” says Greenberg, including several neuropsychiatric conditions, as well as some types of cancer.
For example, when cells contain too many or too few transcription factors such as Fos, learning and memory problems may arise. In multiple myeloma, cancer cells become addicted to the immune protein IRF4, so its presence can trigger disease. Researchers are particularly interested in identifying diseases that may be good candidates for developing therapies that work via the mandulin proteasome pathway.
“One of the areas we are actively exploring is how to tune the specificity of the mechanism so as to be able to analyze the protein of interest specifically,” said Gu.
Reference: “Medulin Proteasome Pathway Captures Protein for Ubiquitin-Independent Degradation” by Shen Guo, Christopher Nardoni, Nolan Kamitaki, Uyo Mao, Stephen J. Eledge, and Michael E. Greenberg, 25 Aug. 2023, Available here. Science.
doi: 10.1126/science.adh5021
Funding was provided by the National Mah Jongg League Fellowship of the Damon Runyon Foundation for Cancer Research, the National Science Foundation Graduate Research Fellowship, and the National Institutes of Health (T32 HG002295; R01 NS115965; AG11085).
2023-08-27 05:50:08
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