Science discovers a "door" into mitochondrial membranes

Mitochondria—organelles responsible for producing energy in human cells—were once free-living organisms that discovered their way
into early eukaryotic cells more than 1 billion years ago.
Since then, they have fused seamlessly with their host like classic examples of symbiotic evolution, and now they rely on the many proteins produced in the host cell nucleus to function properly
.

Proteins on the outer mitochondrial membrane are especially important; They allow mitochondria to communicate with the rest of the cell and play a role
in immune function and a type of programmed cell death called apoptosis.
In the process of evolution, cells evolved a special mechanism by which these proteins produced in the cytoplasm of the cell were inserted into the mitochondrial membrane
.
But what this mechanism is, and which cells are involved, has always been a mystery
.

A new paper by Whitehead Institute member Jonathan Weissman and Caltech professor Rebecca Voorhees provides the answer
to this puzzle.
The study was published Oct.
21 in
the journal Science.
The study revealed a protein called mitochondrial carrier homologate 2 (MTCH2 for short), which has been implicated in many cellular processes and even diseases such as cancer and Alzheimer's disease, responsible for acting as a "gate"
for various proteins to enter the mitochondrial membrane.

"So far, no one knows exactly what MTCH2 is doing — they just know that when you lose it, all these different things happen to the cells," said Weissman, who is also a professor of biology at MIT and a researcher
at the Howard Hughes Medical Institute.
"Why this protein affects so many different processes is a bit of a mystery
.
This study provides the molecular basis for understanding why MTCH2 is associated with Alzheimer's disease, lipid biosynthesis, and mitochondrial fission and fusion: because it is responsible for inserting all these different types of proteins into membranes
.
”

"The collaboration between our labs is critical to understanding the biochemistry of this interaction and has led to a truly exciting new understanding
of a fundamental question in cell biology," Voorhees said.

Look for a door

To find out how proteins in the cytoplasm—specifically a protein known as tail anchoring—are inserted into the outer mitochondrial membrane, Alina Guna, a postdoctoral researcher in Whitehead's lab and first author of the study, along with Taylor Stevens, a graduate student in Voorhees' lab, and Alison Inglis, a postdoc, decided to use a technique called CRISPR interference, or CRISPRi, screening method.
The technique was invented by Weissman and collaborators
.

Guna said: "CRISPRi allows us to systematically remove each gene and then observe what happens
[to a specific tail anchoring protein].
We found a gene called MTCH2, and when we remove it, the amount of protein that reaches the mitochondrial membrane is drastically reduced
.
So we thought, maybe this is the entrance
to entry.
”

To confirm MTCH2 as a gateway into the mitochondrial membrane, the researchers conducted additional experiments to see what happens
when MTCH2 is not present in the cell.
They found that MTCH2 is a necessary and sufficient condition
for tail anchor membrane proteins to enter the mitochondrial membrane from the cytoplasm.

MTCH2's ability to transport proteins from the cytoplasm to the mitochondrial membrane may be due to its special shape
.
The researchers tested
the protein's sequence with an alpha fold system.
The alpha folding system is an artificial intelligence system that predicts the structure of a protein from its amino acid sequence, and it turns out that it is a hydrophobic protein — ideal for inserting into oily membranes — but has a hydrophilic tank that other proteins can enter
.

"It's basically like a funnel
," Guna said.
Proteins come from the cytoplasm, they slide into the hydrophilic trough, and then move from the protein to the membrane
.
”

To confirm that this groove is important in the function of proteins, Guna and her colleagues designed another experiment
.
"We wanted to try the structure and see if we could change its behavior, and we did
," Guna said.
We performed a single point mutation that was enough to really change the behavior of the protein and its interaction
with the substrate.
Then we continued our research and found mutations that made it less active and mutations
that made it super active.
”

The application of this new study goes beyond answering a fundamental question
in mitochondrial research.
Guna said, "This thing brings a lot of things
.
"

On the one hand, MTCH2 inserts a key protein called apoptosis programmed cell death, which researchers may use to treat cancer
.
"We can make leukemia cells more sensitive to cancer treatment by mutating them that alter the activity of MTCH2," Guna said
.
"This mutation makes MTCH2 behavior more 'voracious,' inserting more stuff into the cell membrane, and some of the stuff is like pro-apoptotic factor, so these cells are more likely to die, which is great in the context of
cancer treatment.
"

This work also raises the question of
how MTCH2 has evolved its capabilities over time.
MTCH2 evolved from a family of proteins called solute vectors, which transport various substances
across cell membranes.

Researchers still need to learn about how mitochondria interact with other parts of the cell, including how they respond to stress and changes within the cell, and how proteins initially find their way into mitochondria
.
"I think [the paper] is just the first step, and this only applies to one class of membrane proteins — it doesn't tell you all the steps
that happen after the protein is made in the cytoplasm.
" For example, how are they transported to mitochondria? So stay tuned – I think we'll learn that we now have a really good system to open up this fundamental part
of cell biology.
”

MTCH2 is a mitochondrial outer membrane protein insertase