This mechanism breaks down short-lived proteins that support brain and immune function.
Short-lived proteins regulate gene expression in cells and play important roles ranging from helping the brain connect to boosting the body’s immune response. These nuclear-generated proteins are rapidly degraded after they have served their purpose.
The mechanisms behind the degradation and removal of these essential proteins from cells have remained a mystery to researchers for decades, to this day.
In an interdisciplinary collaboration, researchers at Harvard Medical School have identified a protein called midorin that plays a key role in the degradation of many short-lived nuclear proteins. This study shows that midorin does so by directly seizing proteins and pulling them into the cell’s waste disposal system called the proteasome, where they are destroyed.
The results of this study were recently published in a journal science.
“These particular short-lived proteins have been known for more than 40 years, but no one has established how they are actually degraded,” said co-first author and neurobiology researcher at HMS. Xin Gu said.
Because proteins degraded by this process regulate genes with important functions related to the brain, immune system, and development, scientists are ultimately targeting this process as a way to control protein levels, You may be able to change these functions and fix malfunctions.
“The mechanism we found is very simple and very elegant,” added co-first author Christopher Nardon, a PhD candidate in genetics at HMS. “This is a fundamental scientific discovery, but it has many implications for the future.”
molecular mystery
It is well established that cells can degrade proteins by tagging them with small molecules called ubiquitin. The tag tells the proteasome that the protein is no longer needed and destroys it. Much of the pioneering work on this process was done by the late Fred Goldberg of HMS.
However, because the proteasome can degrade proteins without the aid of ubiquitin tags, researchers suspect that there may be other, ubiquitin-independent mechanisms of protein degradation.
“There was sporadic evidence in the literature that somehow the proteasome could directly degrade unmarked proteins, but no one understood how that happened,” Nardon said. .
One group of proteins that are thought to be degraded by a different mechanism are stimulus-inducible transcription factors. Proteins are rapidly produced in response to cellular stimuli, translocate to the cell’s nucleus to turn on genes, and are then rapidly destroyed.
“The first thing that strikes me is that these proteins are very unstable and have very short half-lives. said Gu.
These transcription factors support a variety of important biological processes in the body, but even after decades of research, “the mechanisms of transcription factor turnover remained largely unknown,” says HMS. said Michael Greenberg, Nathan Marsh Pusey, professor of neurobiology at the Bravatnik Institute. The paper’s co-senior author is Gregor Mendel, Professor of Genetics and Medicine at HMS and Brigham and Women’s Hospital, where he co-authored with Stephen Elledge.
from a few to hundreds
To investigate this mechanism, the team started with two well-known transcription factors. Fos has been extensively studied by the Greenberg lab for its role in learning and memory, another is her EGR1 involved in cell division and survival. Using advanced protein and genetic analysis developed in the Elledge lab, the researchers focused on midorin as a protein that helps degrade both transcription factors. Follow-up experiments revealed that in addition to Fos and his EGR1, midorin may also be involved in the degradation of hundreds of other transcription factors in the nucleus.
Gu and Nardone recall being shocked and skeptical of their results. To confirm their findings, they decided they needed to figure out exactly how midorin targets and degrades so many different proteins.
“After identifying all these proteins, a lot of puzzling questions arose about how midorin’s mechanism actually works,” Nardon said.
with the help of machine learning Using a tool called AlphaFold, which predicts protein structure, and the results of a series of lab experiments, the team was able to flesh out the details of the mechanism. They established that midorin has a ‘catch domain’. This is the region of the protein that traps other proteins and sends them directly to the proteasome where they are degraded. This Catch domain is amino acid This allows midorin to capture a wide variety of proteins, as it captures relatively unstructured regions of proteins.
Of note are proteins like Fos, which are responsible for turning on genes that encourage neurons in the brain to wire and rewire themselves in response to stimuli. Other proteins, such as IRF4, activate genes that support the immune system by ensuring cells can make functional B and T cells.
“The most interesting aspect of this work is that we now understand a new general mechanism for protein degradation that does not depend on ubiquitination,” Eledge said.
Fascinating translation possibilities
In the short term, researchers hope to delve even deeper into the mechanisms they have discovered. They plan structural studies to better understand the details of how midorin traps and degrades proteins. They are also creating mice lacking midorin to understand the protein’s role in different cells and developmental stages.
The scientists say their findings have interesting translational potential. This provides a pathway that researchers can exploit to control the levels of transcription factors, thereby potentially regulating gene expression and thus related processes in the body.
“Protein breakdown is an important process, and its deregulation underlies many disorders and diseases, including certain neurological and psychiatric disorders and some cancers,” Greenberg said.
For example, too much or too little transcription factors such as Fos in cells can lead to learning and memory problems. In multiple myeloma, cancer cells become dependent on the immune protein IRF4, and its presence may drive disease. Researchers are particularly interested in identifying diseases that may be potential candidates for therapeutic development that act through the Mindrin-proteasome pathway.
“One of the areas we are actively researching is how to tune the specificity of the mechanism to specifically degrade the protein of interest,” Gu said.
Reference: “Midonoline-proteasome pathway traps proteins for ubiquitination-independent degradation,” Xin Gu, Christopher Nardone, Nolan Kamitaki, Aoyue Mao, Stephen J. Elledge, Michael E. Greenberg, August 2023 25th, science.
DOI: 10.1126/science.adh5021
Funding came from the Damon Runyon Cancer Research Foundation’s National Mahjong League Fellowship, a National Science Foundation Graduate Research Fellowship, and National Institutes of Health (T32 HG002295; R01 NS115965; AG11085).