Unfolding Story

Under protein-folding stress, mitochondria activate a two-pronged defense

Artistic depiction of mitochondrial damages in an increasingly harmful environment (left to right). Image: Harper lab

Artistic depiction of mitochondrial damages in an increasingly harmful environment (left to right). Image: Harper lab

The mitochondria within a cell are small structures that play an outsized role. They convert oxygen and simple sugars into ATP, the cell’s source of energy, actions essential to metabolic pathways and a cell’s very survival.

“Given the importance of mitochondria in human health, it is important to understand the mechanisms underlying their ability to cope with protein-folding stress.”—Wade Harper

The generation of ATP occurs through a series of large membrane-associated protein complexes in mitochondria that make up the electron transport chain. This system represents a vestige of the energy-producing system of bacteria that merged with single-celled microorganisms 1.5 billion years ago and evolved into mitochondria. During this process, genes encoding several proteins of the electron transport chain were transferred to the nuclear genome of the cell while others were retained in a much smaller mitochondrial genome.

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This compartmentalization of genetic information necessitates three major steps for producing the electron transport chain: synthesis of nuclear DNA-encoded proteins in the cytoplasm, followed by transport of these proteins into mitochondria and then the assembly of these proteins with complementary proteins encoded by the mitochondrial genome and produced within mitochondria.Gene ontology enrichment map depicting functional clusters of mitochondrial proteins regulated by the mitochondrial unfolded protein response. Image: Harper lab

Given this complexity, errors in production are frequent. So mitochondria rely upon mechanisms that sense defective protein folding and attempt to correct errors in order to remain healthy.

This sensing system, referred to as the mitochondrial “unfolded protein response,” has been studied extensively in the nematode worm C. elegans using genetic tools, which led to the identification of a network of genes that allows communication between the mitochondria and gene expression pathways in the nucleus.

Much less is known concerning how this system is organized in mammals, although the sentinel “chaperonin” proteins encoded in the nucleus and known to be induced in C. elegans are also induced in mammalian cells when proteins misfold in mitochondria.

Now, Wade Harper and Christian Münch, two Harvard Medical School scientists, describe the global response of mammalian cells to mitochondrial protein-folding stress at both the level of the nuclear transcriptional response and the local changes in protein synthesis within mitochondria itself. Their study appeared June 22 in Nature.

“Given the importance of mitochondria in human health, it is important to understand the mechanisms underlying their ability to cope with protein-folding stress,” said Harper, the HMS Bert and Natalie Vallee Professor of Molecular Pathology, head of the Department of Cell Biology and senior author of the paper. “This study provides a framework for beginning to understand this process in greater detail in humans.”

In their experiments, Münch, an HMS research fellow in cell biology and first author of the study, created acute stress by inhibiting proteins directly involved in the folding or degradation of misfolded proteins, leading to the accumulation of misfolded proteins in mitochondria.

Analysis of gene expression revealed alterations in hundreds of nuclear genes, including many that encode proteins known to localize in mitochondria, such as chaperonins. This process marks the first arm of the unfolded protein response intended to maintain protein folding within the mitochondria, and indicates a broad underlying transcriptional response.

In order to understand the status of the mitochondrial proteome, Münch used state-of-the-art quantitative mass spectrometry to analyze proteins in mitochondria undergoing protein-folding stress. Dozens of mitochondrial proteins change in abundance, including proteins linked with protein synthesis and folding in mitochondria.

“It’s a comprehensive look at what really changes in mammalian cells if you induce mitochondrial protein-folding stress,” Münch said.

One protein looked particularly interesting in these analyses: MRPP3, a component of the mitochondrial RNase P complex that mitochondria need to process RNA to produce messenger RNA and transfer RNA for use in the translation of proteins encoded by the mitochondrial genome.

“This is a novel pathway through which mitochondria transiently and locally respond to mitochondrial protein misfolding.”—Christian Münch

When the scientists induced stress, MRPP3 levels were reduced, and this resulted in a decrease in processing of messenger and transfer RNA inside mitochondria. Moreover, the team found that the synthesis of proteins within mitochondria was dramatically blocked upon mitochondrial stress, revealing for the first time that protein synthesis within mitochondria is a major target of the response to protein misfolding within mitochondria.

Much like the unfolded protein response in a more widely studied organelle, the endoplasmic reticulum, protein misfolding within the mitochondria promotes a two–pronged attack, reducing the protein folding “load” by reducing translation and promoting protein folding through induction of chaperonins.

“This is a novel pathway through which mitochondria transiently and locally respond to mitochondrial protein misfolding,” Münch said.

This study now opens up the opportunity to understand in greater detail how signals are transmitted from mitochondria to the nucleus in mammals and also how protein synthesis pathways in mitochondria interface with the protein-folding machinery. The work may also provide new markers to understand the mitochondrial unfolded protein response in disease, including neurodegenerative diseases that often display mitochondrial dysfunction.

This work was supported by National Institutes of Health grant R37NS083524, Biogen Inc. and an EMBO Fellowship. Harper is a consultant for Biogen.