Information

Do mitochondria contain the genes to specify themselves?


My book says : "Mitochondria contain their own genetic material so when a cell divides, the mitochondria replicate themselves under the control of the nucleus." The book means that the mitochondria contain the genes which produce the mitochondria right ?


The answer is a bit more complicated than that. Mitochondria contain their own genome called mitochondrial DNA (mtDNA), encoding 13 proteins that are part of respiratory complexes I, III, IV, and V, 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The separate tRNAs and rRNAs are necessary because the mitochondrial genome uses a slightly different genetic code than the nuclear genome.

So, the mitochondria contain nearly all of the genes necessary to construct the respiratory chain, as well as the machinery to translate the mRNA into protein. However, it does not contain any of the genes necessary to actually replicate the mtDNA (DNA polymerases, etc.) or construct the mitochondrion itself - synthesize the components of the different membranes, arrange the membranes in their required conformation, chaperones to assemble the complexes of the respiratory chain, etc. - these are all encoded in the nuclear DNA.


The origin and early evolution of mitochondria

Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial (specifically α-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome.

Recent debates about eukaryotic cell evolution have been closely connected to the issue of how mitochondria originated and have evolved [1,2,3,4,5,6,7]. These debates have posed such questions as the following: Did the mitochondrion arise at the same time as, or subsequent to, the rest of the eukaryotic cell? Did it originate under initially anaerobic or aerobic conditions? What is the evolutionary relationship between mitochondria and hydrogenosomes (H2-generating and ATP-producing organelles that are found in eukaryotes lacking mitochondria)? Is the amitochondrial condition in these organisms a secondary adaptation or is it evolutionarily primitive - or, in other words, did any organisms diverge from the main line of eukaryotic evolution before the advent of mitochondria? Whereas the issue of how the eukaryotic cell arose remains controversial [8,9], current genomic data do allow us to make a number of reasonably compelling inferences about how mitochondria themselves originated and have since evolved.


Methods of Inheritance

An individual may inherit a mitochondrial disease in one of many ways. How a disease is inherited, depends upon where the mutation exists. Wherever there is DNA, there is a potential source for a mutation. In a human cell there exist not one, but two full genomes. The first is the human genome located in the nucleus of the cell, where DNA is organized into structures called chromosomes. The second is mitochondrial DNA (mtDNA) which is located in the organelle after which it is named.

NUCLEAR DNA DISEASES

What is the source of the problem?
Our DNA inside the nucleus is our entire body’s blueprint which we inherit from both of our parents. It is organized into two sets of 23 chromosomes (one set from each parent). Along the chromosomes are genes. An average human genome contains approximately 26 000 genes. A small fraction of those nuclear genes code for mitochondrial proteins, therefore a mutation in one of these genes could lead to mitochondrial disease.

If there is a mutation in a nuclear gene in my parents, what are the chances of me inheriting the mutation or the disease?
Recall that we have two copies of each chromosome—one from each parent. Both chromosomes contain the same genes and code for the same proteins, just slightly different versions of it. An example is eye colour both parents have genes coding for eye colour yet the father may have the version for blue eyes and the mother may have the version coding for brown eyes. These different gene versions are called alleles. Variation exists within everyone’s genes—that is how we are all different. However, some genetic changes (or mutations) can cause the gene to not function properly and thereby cause disease. Genetic changes leading to disease are inherited in my different ways. The chance of being affected with a disease depends on many factors which are outlined below.


Autosomal Dominant
Like its namesake, autosomal dominant inheritance occurs because one allele “dominates” over the other. Of the two alleles, one genetic change on one allele will result in the condition being expressed, even if the other allele does not have a genetic change. This also means that at least one parent may also have the disease. The images below show possible scenarios:

As seen above, having one affected parent who has both versions of the harmful allele, may give the disease to all their children. In contrast, a parent with only one version of the harmful allele may pass down the disease to only 50% of children.


Autosomal Recessive
To acquire an autosomal recessive disease, both alleles in a person need to have a mutation. In autosomal recessive diseases the parents are known as carriers because only one of their genes has a mutation. Carriers are commonly asymptomatic (they do not show any signs of the disease), yet they carry a gene mutation that they can pass down to their children. It is common for the parents of a person with an autosomal recessive disease to be a carrier yet have no family history of the disease. The possible scenarios for inheriting autosomal recessive diseases are shown below:
The four scenarios in autosomal recessive diseases:

As seen above, it is only possible to inherit a recessive disease when a mutation exists on both sides of the family.


MITOCHONDRIAL DNA DISEASES

Where is the genetic change?
As previously discussed, there are two sources of DNA in our body existing in two genomes—the nuclear DNA and mitochondrial DNA. Mitochondria are of course the energy producing organelles in the body.


Mitochondria have their own set of instructions, or blueprints—they have their own set of DNA. Mitochondrial DNA (mtDNA) contains genes that code for a number of proteins that are used by mitochondria (i.e. the proteins of the respiratory chain). Changes in mtDNA are another potential source of mitochondrial disease.


The inheritance of mtDNA is very different from the inheritance of nuclear DNA. It follows a pattern known as maternal inheritance. The process of conception and the relative contribution of materials from the sperm and the egg can help explain the concept. Sperm cells do not have mitochondria therefore MtDNA is not present in these cells, meaning the father will only contribute nuclear DNA and will not contribute any mtDNA. On the other hand, many mitochondria are present in a woman’s egg therefore mtDNA from the mother is passed down to the next generation (in addition to nuclear DNA). Consequently if a mother has changes (mutations) in her mtDNA, these can be inherited by offspring. Essentially, mitochondrial diseases caused by mutations in the mtDNA can only be inherited from the mother, not the father.

The images of the pedigrees below illustrate this concept:

An father (left) would not pass down his mtDNA but a mother passes down all her mitochondrial traits to her children (right)

If there is a mutation in my parents’ mitochondrial DNA, what are the chances that I will inherit the mutation or be affected by the disease?
The answer to this question depends on which parent has a change in their mtDNA. If the mutation/disease is in the father, it will not be passed down.
If it occurs in the mother, the mutation will almost always be passed down but the effects of the disease can be variable in the next generation. This occurs due to a phenomenon known as heteroplasmy.

As indicated above, mitochondria are present in a woman’s egg cell, as well as other cells in the body. At the conception of a child, the woman’s egg and the man’s sperm combine to form one complete genetic complement. Recall that all the mitochondria in this newly formed embryo are inherited from the mother.

All cells go through a process of cell division, including a developing embryo, which divides a cell into two distinct cells. During cell division, mitochondria are randomly dispersed throughout the cell. When a cell divides, the mitochondria present are divided randomly based on their positioning within the cell during division. If there is a mtDNA mutation present in any of the mitochondria, these can be divided into the newly formed cell. Based on the random nature of the dispersion of the mitochondria within the cell, there is sometimes an uneven distribution of mitochondria in these divided cells—some with mtDNA mutations and other without such mutations. If the patient has a disproportionate amount of mtDNA with mutations, the patient may surpass the threshold effect and express the disease.

Whether the next generation will be affected by the disease depends upon how mitochondria have divided themselves into the female’s ova. This is illustrated below in the image
ANIMATION

Each cell contains many mitochondria likewise, each mitochondrion contains many copies of DNA. This leads to the concept of threshold effect. A certain number of mutation in the mtDNA must be present in any cell in order for symptoms to occur, at which time the “threshold” is overcome).

X-linked Inheritance

X-linked Inheritance involves the sex chromosomes, X and Y, which are present in the nuclear genome. Recall that a female has two X chromosomes, while males have one X and one Y. When there is a genetic change in one of the genes of the X chromosome the inheritance is said to be X-linked.
Males are more likely to express an X-linked condition because they have one X and one Y chromosome. When males inherit a genetic change on their X chromosome, they do not have a second copy of the gene whereas females have two X chromosomes and therefore two copies of each gene. Therefore, if a female were to inherit a genetic change along her X chromosome, she would be a carrier for that associated condition. Females with a mutation present on both copies of a gene present on her X chromosomes would be affected with the associated disease.
Interestingly, there is a phenomenon known as “X-inactivation” or “Lyonization” that renders one copy of each of a female’s X-chromosomes inactive. This occurs early in the process of the development of the fetus. If the female’s X-inactivation is “skewed,” to include more inactive copies of the “normal” gene, then this female may exhibit some symptoms of the condition, while genetically she would be said to be a carrier. This phenomenon explains why some women who are carriers of an X-linked condition display symptoms of the disease, albeit typically less severe than their male counterparts.
This is illustrated below.


Inheritance

Mitochondrial complex I deficiency has several inheritance patterns, depending on the gene involved. When the disorder is caused by a mutation in a gene found in nuclear DNA, it has autosomal recessive or X-linked inheritance. Autosomal recessive means that both copies of the gene in each cell have mutations. The parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene, but they typically do not show signs and symptoms of the condition because the other copy of the gene is normal.

X-linked inheritance occurs when the mutated gene that causes the disorder is located on the X chromosome, one of the two sex chromosomes in each cell. In males, who have only one X chromosome, a mutation in the only copy of the gene in each cell is sufficient to cause the condition. In females, who have two copies of the X chromosome, one altered copy of the gene in each cell can lead to less severe features of the condition or may cause no signs or symptoms at all. A characteristic of X-linked inheritance is that fathers cannot pass X-linked traits to their sons.

When mitochondrial complex I deficiency is caused by a mutation in a gene found in mtDNA, it is inherited in a mitochondrial pattern , which is also known as maternal inheritance. Because egg cells, but not sperm cells, contribute mitochondria to the developing embryo, children can inherit disorders resulting from mtDNA mutations only from their mother. These disorders can appear in every generation of a family and can affect both males and females, but fathers do not pass traits associated with changes in mtDNA to their children.


Origin

As mitochondria contain ribosomes and DNA, and are only formed by the division of other mitochondria, it is generally accepted that they were originally derived from endosymbiotic prokaryotes. Studies of mitochondrial DNA, which is often circular and employs a variant genetic code, show their ancestor, the so-called proto-mitochondrion, was a member of the Proteobacteria. In particular, the pre-mitochondrion was probably related to the rickettsias, although the exact position of the ancestor of mitochondria among the alpha-proteobacteria remains controversial. The endosymbiotic hypothesis suggests that mitochondria descended from specialized bacteria (probably purple non-sulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm. The ability of symbiont bacteria to conduct cellular respiration in host cells that had relied on glycolysis and fermentation would have provided a considerable evolutionary advantage. Similarly, host cells with symbiotic bacteria capable of photosynthesis would also have an advantage. In both cases, the number of environments in which the cells could survive would have been greatly expanded.

This relationship developed at least 2 billion years ago and mitochondria still show some signs of their ancient origin. Mitochondrial ribosomes are the 70S (bacterial) type, in contrast to the 80S ribosomes found elsewhere in the cell. As in prokaryotes, there is a very high proportion of coding DNA, and an absence of repeats. Mitochondrial genes are transcribed as multigenic transcripts which are cleaved and polyadenylated to yield mature mRNAs. Unlike their nuclear cousins, mitochondrial genes are small, generally lacking introns, and many chromosomes are circular, conforming to the bacterial pattern.

A few groups of unicellular eukaryotes lack mitochondria: the microsporidians, metamonads, and archamoebae. On rRNA trees these groups appeared as the most primitive eukaryotes, suggesting they appeared before the origin of mitochondria, but this is now known to be an artifact of long branch attraction &mdash they are apparently derived groups and retain genes or organelles derived from mitochondria (e.g. mitosomes and hydrogenosomes). There are no primitively amitochondriate eukaryotes, and so the origin of mitochondria may have played a critical part in the development of eukaryotic cells.


Biologists Discover Pathway That Protects Mitochondria

MIT biologists have discovered the first cellular response targeted at helping mitochondria when their protein import goes wrong. Image courtesy of the researchers and Ella Maru Studio.

MIT Scientists discover a pathway that monitors a protein import into mitochondria and elicits a cellular response when the process goes awry.

If there’s one fact that most people retain from elementary biology, it’s that mitochondria are the powerhouses of the cell. As such, they break down molecules and manufacture new ones to generate the fuel necessary for life. But mitochondria rely on a stream of proteins to sustain this energy production. Nearly all their proteins are manufactured in the surrounding gel-like cytoplasm, and must be imported into the mitochondria to keep the powerhouse running.

A duo of MIT biologists has revealed what happens when a traffic jam of proteins at the surface of the mitochondria prevents proper import. They describe how the mitochondria communicate with the rest of the cell to signal a problem, and how the cell responds to protect the mitochondria. This newly-discovered molecular pathway, called mitoCPR, detects import mishaps and preserves mitochondrial function in the midst of such stress.

“This is the first mechanism identified that surveils mitochondrial protein import, and helps mitochondria when they can’t get the proteins they need,” says Angelika Amon, the Kathleen and Curtis Marble Professor of Cancer Research in the MIT Department of Biology, who is also a member of the Koch Institute for Integrative Cancer Research at MIT, a Howard Hughes Medical Institute Investigator, and senior author of the study. “Responses to mitochondrial stress have been established before, but this one specifically targets the surface of the mitochondria, clearing out the misfolded proteins that are stuck in the pores.”

Hilla Weidberg, a postdoc in Amon’s lab, is the lead author of the study, which appears in Science on April 13.

Fueling the powerhouse

Mitochondria likely began as independent entities long ago, before being engulfed by host cells. They eventually gave up control and moved most of their important genes to a different organelle, the nucleus, where the rest of the cell’s genetic blueprint is stored. The protein products from these genes are ultimately made in the cytoplasm outside the nucleus, and then guided to the mitochondria. These “precursor” proteins contain a special molecular zip code that guides them through the channels at the surface of the mitochondria to their respective homes.

The proteins must be unfolded and delicately threaded through the narrow channels in order to enter the mitochondria. This creates a precarious situation if the demand is too high, or the proteins are folded when they shouldn’t be, a bottleneck forms that none shall pass. This can simply occur when the mitochondria expand to make more of themselves, or in diseases like deafness-dystonia syndrome and Huntington’s.

“The machinery that we’ve identified seems to evict proteins that are sitting on the surface of the mitochondria and sends them for degradation,” Amon says. “Another possibility is that this mitoCPR pathway might actually unfold these proteins, and in doing so give them a second chance to be pushed through the membrane.”

Two other pathways were recently identified in yeast that also respond to accumulated mitochondrial proteins. However, both simply clear protein refuse from the cytoplasm around the mitochondria, rather than removing the proteins collecting on the mitochondria themselves.

“We knew about various responses to mitochondrial stress, but no one had described a response to protein import defects that specifically protected the mitochondria, and that’s exactly what mitoCPR does,” Weidberg says. “We wanted to know how the cell reacts to these problems, so we set out to overload the import machinery, causing many proteins to rush into the mitochondrion at the same time and clog the pores, triggering a cellular response.”

“What makes our cells absolutely dependent on mitochondria is one of those million-dollar questions in cell biology,” says Vlad Denic, professor of molecular and cellular biology at Harvard University. “This study reveals an interesting flip-side to that question: When you make mitochondrial life artificially tough, are they programmed to say ‘help us’ so the host cell comes to their rescue? The possible ramifications of such work in terms of human development and disease could be very impressive.”

A pathway to understanding

Roughly two decades ago, researchers began to notice that the genes required to defend cells against drugs and other foreign substances — together, called the multidrug resistance (MDR) response — were also expressed in yeast mitochondrial mutants for some unknown reason. This suggested that the protein in charge of binding to the DNA and initiating the MDR response must have a dual purpose, sometimes triggering a second, separate pathway as well. But precisely how this second pathway related to mitochondria remained a mystery.

“Twenty years ago, scientists recognized mitoCPR as some kind of mechanism against mitochondrial dysfunction,” Weidberg says. “Today we’ve finally characterized it, given it a name, and identified its precise function: to help mitochondrial protein import.”

As the import process slows, Amon and Weidberg determined that the protein that initiates mitoCPR — the transcription factor Pdr3 — binds to DNA within the nucleus, inducing the expression of a gene known as CIS1. The resultant Cis1 protein binds to the channel at the surface of the mitochondrion, and recruits yet another protein, the AAA+ adenosine triphosphatase Msp1, to help clear unimported proteins from the mitochondrial surface and mediate their degradation. Although the MDR response pathway differs from that of mitoCPR, both rely on Pdr3 activation. In fact, mitoCPR requires it.

“Whether the two pathways interact with one another is a very interesting question,” Amon says. “The mitochondria make a lot of biosynthetic molecules, and blocking that function by messing with protein import could lead to the accumulation of intermediate metabolites. These can be toxic to the cell, so you could imagine that activating the MDR response might pump out harmful intermediates.”

The question of what activates Pdr3 to initiate mitoCPR is still unclear, but Weidberg has some ideas related to signals stemming from the build-up of toxic metabolite intermediates. It’s also yet to be determined whether an analogous pathway exists in more complex organisms, although there is some evidence that the mitochondria do communicate with the nucleus in other eukaryotes besides yeast.

“This was just such a classic study,” Amon says. “There were no sophisticated high-throughput methodologies, just traditional, simple molecular biology and cell biology assays with a few microscopes. It’s almost like something you’d see out of the 1980s. But that just goes to show — to this day — that’s how many discoveries are made.”

The research was funded by the National Institutes of Health and by the Koch Institute Support (core) Grant from the National Cancer Institute. Amon is also an investigator of the Howard Hughes Medical Institute and the Glenn Foundation for Biomedical Research. Weidberg was supported by the Jane Coffin Childs Memorial Fund, the European Molecular Biology Organization Long-Term Fellowship, and the Israel National Postdoctoral Program for Advancing Women in Science.


Scientists discover a pathway that monitors a protein import into mitochondria

MIT biologists have discovered the first cellular response targeted at helping mitochondria when their protein import goes wrong. Credit: Ella Maru Studio

If there's one fact that most people retain from elementary biology, it's that mitochondria are the powerhouses of the cell. As such, they break down molecules and manufacture new ones to generate the fuel necessary for life. But mitochondria rely on a stream of proteins to sustain this energy production. Nearly all their proteins are manufactured in the surrounding gel-like cytoplasm, and must be imported into the mitochondria to keep the powerhouse running.

A duo of MIT biologists has revealed what happens when a traffic jam of proteins at the surface of the mitochondria prevents proper import. They describe how the mitochondria communicate with the rest of the cell to signal a problem, and how the cell responds to protect the mitochondria. This newly-discovered molecular pathway, called mitoCPR, detects import mishaps and preserves mitochondrial function in the midst of such stress.

"This is the first mechanism identified that surveils mitochondrial protein import, and helps mitochondria when they can't get the proteins they need," says Angelika Amon, the Kathleen and Curtis Marble Professor of Cancer Research in the MIT Department of Biology, who is also a member of the Koch Institute for Integrative Cancer Research at MIT, a Howard Hughes Medical Institute Investigator, and senior author of the study. "Responses to mitochondrial stress have been established before, but this one specifically targets the surface of the mitochondria, clearing out the misfolded proteins that are stuck in the pores."

Hilla Weidberg, a postdoc in Amon's lab, is the lead author of the study, which appears in Science on April 13.

Fueling the powerhouse

Mitochondria likely began as independent entities long ago, before being engulfed by host cells. They eventually gave up control and moved most of their important genes to a different organelle, the nucleus, where the rest of the cell's genetic blueprint is stored. The protein products from these genes are ultimately made in the cytoplasm outside the nucleus, and then guided to the mitochondria. These "precursor" proteins contain a special molecular zip code that guides them through the channels at the surface of the mitochondria to their respective homes.

The proteins must be unfolded and delicately threaded through the narrow channels in order to enter the mitochondria. This creates a precarious situation if the demand is too high, or the proteins are folded when they shouldn't be, a bottleneck forms that none shall pass. This can simply occur when the mitochondria expand to make more of themselves, or in diseases like deafness-dystonia syndrome and Huntington's.

"The machinery that we've identified seems to evict proteins that are sitting on the surface of the mitochondria and sends them for degradation," Amon says. "Another possibility is that this mitoCPR pathway might actually unfold these proteins, and in doing so give them a second chance to be pushed through the membrane."

Two other pathways were recently identified in yeast that also respond to accumulated mitochondrial proteins. However, both simply clear protein refuse from the cytoplasm around the mitochondria, rather than removing the proteins collecting on the mitochondria themselves.

"We knew about various responses to mitochondrial stress, but no one had described a response to protein import defects that specifically protected the mitochondria, and that's exactly what mitoCPR does," Weidberg says. "We wanted to know how the cell reacts to these problems, so we set out to overload the import machinery, causing many proteins to rush into the mitochondrion at the same time and clog the pores, triggering a cellular response."

"What makes our cells absolutely dependent on mitochondria is one of those million-dollar questions in cell biology," says Vlad Denic, professor of molecular and cellular biology at Harvard University. "This study reveals an interesting flip-side to that question: When you make mitochondrial life artificially tough, are they programmed to say 'help us' so the host cell comes to their rescue? The possible ramifications of such work in terms of human development and disease could be very impressive."

A pathway to understanding

Roughly two decades ago, researchers began to notice that the genes required to defend cells against drugs and other foreign substances—together, called the multidrug resistance (MDR) response—were also expressed in yeast mitochondrial mutants for some unknown reason. This suggested that the protein in charge of binding to the DNA and initiating the MDR response must have a dual purpose, sometimes triggering a second, separate pathway as well. But precisely how this second pathway related to mitochondria remained a mystery.

"Twenty years ago, scientists recognized mitoCPR as some kind of mechanism against mitochondrial dysfunction," Weidberg says. "Today we've finally characterized it, given it a name, and identified its precise function: to help mitochondrial protein import."

As the import process slows, Amon and Weidberg determined that the protein that initiates mitoCPR—the transcription factor Pdr3—binds to DNA within the nucleus, inducing the expression of a gene known as CIS1. The resultant Cis1 protein binds to the channel at the surface of the mitochondrion, and recruits yet another protein, the AAA+ adenosine triphosphatase Msp1, to help clear unimported proteins from the mitochondrial surface and mediate their degradation. Although the MDR response pathway differs from that of mitoCPR, both rely on Pdr3 activation. In fact, mitoCPR requires it.

"Whether the two pathways interact with one another is a very interesting question," Amon says. "The mitochondria make a lot of biosynthetic molecules, and blocking that function by messing with protein import could lead to the accumulation of intermediate metabolites. These can be toxic to the cell, so you could imagine that activating the MDR response might pump out harmful intermediates."

The question of what activates Pdr3 to initiate mitoCPR is still unclear, but Weidberg has some ideas related to signals stemming from the build-up of toxic metabolite intermediates. It's also yet to be determined whether an analogous pathway exists in more complex organisms, although there is some evidence that the mitochondria do communicate with the nucleus in other eukaryotes besides yeast.

"This was just such a classic study," Amon says. "There were no sophisticated high-throughput methodologies, just traditional, simple molecular biology and cell biology assays with a few microscopes. It's almost like something you'd see out of the 1980s. But that just goes to show—to this day—that's how many discoveries are made."


Countering mitochondrial stress

If there’s one fact that most people retain from elementary biology, it’s that mitochondria are the powerhouses of the cell. As such, they break down molecules and manufacture new ones to generate the fuel necessary for life. But mitochondria rely on a stream of proteins to sustain this energy production. Nearly all their proteins are manufactured in the surrounding gel-like cytoplasm, and must be imported into the mitochondria to keep the powerhouse running.

A duo of MIT biologists has revealed what happens when a traffic jam of proteins at the surface of the mitochondria prevents proper import. They describe how the mitochondria communicate with the rest of the cell to signal a problem, and how the cell responds to protect the mitochondria. This newly-discovered molecular pathway, called mitoCPR, detects import mishaps and preserves mitochondrial function in the midst of such stress.

“This is the first mechanism identified that surveils mitochondrial protein import, and helps mitochondria when they can't get the proteins they need,” says Angelika Amon, the Kathleen and Curtis Marble Professor of Cancer Research in the MIT Department of Biology, who is also a member of the Koch Institute for Integrative Cancer Research at MIT, a Howard Hughes Medical Institute Investigator, and senior author of the study. “Responses to mitochondrial stress have been established before, but this one specifically targets the surface of the mitochondria, clearing out the misfolded proteins that are stuck in the pores.”

Hilla Weidberg, a postdoc in Amon’s lab, is the lead author of the study, which appears in Science on April 13.

Fueling the powerhouse

Mitochondria likely began as independent entities long ago, before being engulfed by host cells. They eventually gave up control and moved most of their important genes to a different organelle, the nucleus, where the rest of the cell’s genetic blueprint is stored. The protein products from these genes are ultimately made in the cytoplasm outside the nucleus, and then guided to the mitochondria. These “precursor” proteins contain a special molecular zip code that guides them through the channels at the surface of the mitochondria to their respective homes.

The proteins must be unfolded and delicately threaded through the narrow channels in order to enter the mitochondria. This creates a precarious situation if the demand is too high, or the proteins are folded when they shouldn’t be, a bottleneck forms that none shall pass. This can simply occur when the mitochondria expand to make more of themselves, or in diseases like deafness-dystonia syndrome and Huntington’s.

“The machinery that we’ve identified seems to evict proteins that are sitting on the surface of the mitochondria and sends them for degradation,” Amon says. “Another possibility is that this mitoCPR pathway might actually unfold these proteins, and in doing so give them a second chance to be pushed through the membrane.”

Two other pathways were recently identified in yeast that also respond to accumulated mitochondrial proteins. However, both simply clear protein refuse from the cytoplasm around the mitochondria, rather than removing the proteins collecting on the mitochondria themselves.

“We knew about various responses to mitochondrial stress, but no one had described a response to protein import defects that specifically protected the mitochondria, and that’s exactly what mitoCPR does,” Weidberg says. “We wanted to know how the cell reacts to these problems, so we set out to overload the import machinery, causing many proteins to rush into the mitochondrion at the same time and clog the pores, triggering a cellular response.”

“What makes our cells absolutely dependent on mitochondria is one of those million-dollar questions in cell biology,” says Vlad Denic, professor of molecular and cellular biology at Harvard University. “This study reveals an interesting flip-side to that question: When you make mitochondrial life artificially tough, are they programmed to say ‘help us’ so the host cell comes to their rescue? The possible ramifications of such work in terms of human development and disease could be very impressive.”

A pathway to understanding

Roughly two decades ago, researchers began to notice that the genes required to defend cells against drugs and other foreign substances — together, called the multidrug resistance (MDR) response — were also expressed in yeast mitochondrial mutants for some unknown reason. This suggested that the protein in charge of binding to the DNA and initiating the MDR response must have a dual purpose, sometimes triggering a second, separate pathway as well. But precisely how this second pathway related to mitochondria remained a mystery.

“Twenty years ago, scientists recognized mitoCPR as some kind of mechanism against mitochondrial dysfunction,” Weidberg says. “Today we’ve finally characterized it, given it a name, and identified its precise function: to help mitochondrial protein import.”

As the import process slows, Amon and Weidberg determined that the protein that initiates mitoCPR — the transcription factor Pdr3 — binds to DNA within the nucleus, inducing the expression of a gene known as CIS1. The resultant Cis1 protein binds to the channel at the surface of the mitochondrion, and recruits yet another protein, the AAA+ adenosine triphosphatase Msp1, to help clear unimported proteins from the mitochondrial surface and mediate their degradation. Although the MDR response pathway differs from that of mitoCPR, both rely on Pdr3 activation. In fact, mitoCPR requires it.

“Whether the two pathways interact with one another is a very interesting question,” Amon says. “The mitochondria make a lot of biosynthetic molecules, and blocking that function by messing with protein import could lead to the accumulation of intermediate metabolites. These can be toxic to the cell, so you could imagine that activating the MDR response might pump out harmful intermediates.”

The question of what activates Pdr3 to initiate mitoCPR is still unclear, but Weidberg has some ideas related to signals stemming from the build-up of toxic metabolite intermediates. It’s also yet to be determined whether an analogous pathway exists in more complex organisms, although there is some evidence that the mitochondria do communicate with the nucleus in other eukaryotes besides yeast.

“This was just such a classic study,” Amon says. “There were no sophisticated high-throughput methodologies, just traditional, simple molecular biology and cell biology assays with a few microscopes. It’s almost like something you’d see out of the 1980s. But that just goes to show — to this day — that’s how many discoveries are made.”

The research was funded by the National Institutes of Health and by the Koch Institute Support (core) Grant from the National Cancer Institute. Amon is also an investigator of the Howard Hughes Medical Institute and the Glenn Foundation for Biomedical Research. Weidberg was supported by the Jane Coffin Childs Memorial Fund, the European Molecular Biology Organization Long-Term Fellowship, and the Israel National Postdoctoral Program for Advancing Women in Science.


Scientists discover a pathway that monitors a protein import into mitochondria

If there’s one fact that most people retain from elementary biology, it’s that mitochondria are the powerhouses of the cell. As such, they break down molecules and manufacture new ones to generate the fuel necessary for life. But mitochondria rely on a stream of proteins to sustain this energy production. Nearly all their proteins are manufactured in the surrounding gel-like cytoplasm, and must be imported into the mitochondria to keep the powerhouse running.

A duo of MIT biologists has revealed what happens when a traffic jam of proteins at the surface of the mitochondria prevents proper import. They describe how the mitochondria communicate with the rest of the cell to signal a problem, and how the cell responds to protect the mitochondria. This newly-discovered molecular pathway, called mitoCPR, detects import mishaps and preserves mitochondrial function in the midst of such stress.

“This is the first mechanism identified that surveils mitochondrial protein import, and helps mitochondria when they can’t get the proteins they need,” says Angelika Amon, the Kathleen and Curtis Marble Professor of Cancer Research in the MIT Department of Biology, who is also a member of the Koch Institute for Integrative Cancer Research at MIT, a Howard Hughes Medical Institute Investigator, and senior author of the study. “Responses to mitochondrial stress have been established before, but this one specifically targets the surface of the mitochondria, clearing out the misfolded proteins that are stuck in the pores.”

Hilla Weidberg, a postdoc in Amon’s lab, is the lead author of the study, which appears in Science on April 13.

Stay on top of the latest Science News. Learn about biology , and the other interesting topics. Subscribe for free »

Mitochondria likely began as independent entities long ago, before being engulfed by host cells. They eventually gave up control and moved most of their important genes to a different organelle, the nucleus, where the rest of the cell’s genetic blueprint is stored. The protein products from these genes are ultimately made in the cytoplasm outside the nucleus, and then guided to the mitochondria. These “precursor” proteins contain a special molecular zip code that guides them through the channels at the surface of the mitochondria to their respective homes.

The proteins must be unfolded and delicately threaded through the narrow channels in order to enter the mitochondria. This creates a precarious situation if the demand is too high, or the proteins are folded when they shouldn’t be, a bottleneck forms that none shall pass. This can simply occur when the mitochondria expand to make more of themselves, or in diseases like deafness-dystonia syndrome and Huntington’s.

“The machinery that we’ve identified seems to evict proteins that are sitting on the surface of the mitochondria and sends them for degradation,” Amon says. “Another possibility is that this mitoCPR pathway might actually unfold these proteins, and in doing so give them a second chance to be pushed through the membrane.”

Two other pathways were recently identified in yeast that also respond to accumulated mitochondrial proteins. However, both simply clear protein refuse from the cytoplasm around the mitochondria, rather than removing the proteins collecting on the mitochondria themselves.

“We knew about various responses to mitochondrial stress, but no one had described a response to protein import defects that specifically protected the mitochondria, and that’s exactly what mitoCPR does,” Weidberg says. “We wanted to know how the cell reacts to these problems, so we set out to overload the import machinery, causing many proteins to rush into the mitochondrion at the same time and clog the pores, triggering a cellular response.”

“What makes our cells absolutely dependent on mitochondria is one of those million-dollar questions in cell biology,” says Vlad Denic, professor of molecular and cellular biology at Harvard University. “This study reveals an interesting flip-side to that question: When you make mitochondrial life artificially tough, are they programmed to say ‘help us’ so the host cell comes to their rescue? The possible ramifications of such work in terms of human development and disease could be very impressive.”

A pathway to understanding

Roughly two decades ago, researchers began to notice that the genes required to defend cells against drugs and other foreign substances—together, called the multidrug resistance (MDR) response—were also expressed in yeast mitochondrial mutants for some unknown reason. This suggested that the protein in charge of binding to the DNA and initiating the MDR response must have a dual purpose, sometimes triggering a second, separate pathway as well. But precisely how this second pathway related to mitochondria remained a mystery.

“Twenty years ago, scientists recognized mitoCPR as some kind of mechanism against mitochondrial dysfunction,” Weidberg says. “Today we’ve finally characterized it, given it a name, and identified its precise function: to help mitochondrial protein import.”

As the import process slows, Amon and Weidberg determined that the protein that initiates mitoCPR—the transcription factor Pdr3—binds to DNA within the nucleus, inducing the expression of a gene known as CIS1. The resultant Cis1 protein binds to the channel at the surface of the mitochondrion, and recruits yet another protein, the AAA+ adenosine triphosphatase Msp1, to help clear unimported proteins from the mitochondrial surface and mediate their degradation. Although the MDR response pathway differs from that of mitoCPR, both rely on Pdr3 activation. In fact, mitoCPR requires it.

“Whether the two pathways interact with one another is a very interesting question,” Amon says. “The mitochondria make a lot of biosynthetic molecules, and blocking that function by messing with protein import could lead to the accumulation of intermediate metabolites. These can be toxic to the cell, so you could imagine that activating the MDR response might pump out harmful intermediates.”

The question of what activates Pdr3 to initiate mitoCPR is still unclear, but Weidberg has some ideas related to signals stemming from the build-up of toxic metabolite intermediates. It’s also yet to be determined whether an analogous pathway exists in more complex organisms, although there is some evidence that the mitochondria do communicate with the nucleus in other eukaryotes besides yeast.

“This was just such a classic study,” Amon says. “There were no sophisticated high-throughput methodologies, just traditional, simple molecular biology and cell biology assays with a few microscopes. It’s almost like something you’d see out of the 1980s. But that just goes to show—to this day—that’s how many discoveries are made.”

Provided by:
Massachusetts Institute of Technology

More information:
Hilla Weidberg et al. MitoCPR—A surveillance pathway that protects mitochondria in response to protein import stress. Science (2018). DOI: 10.1126/science.aan4146

Image:
MIT biologists have discovered the first cellular response targeted at helping mitochondria when their protein import goes wrong
Credit: Ella Maru Studio


A sexual conflict that led to the sexes

There is evidence that this conflict dates back to the days when all organisms were made of single cells. Male and female sexes did not exist, because all reproductive cells were of the same size.

“One of the strategies an organism can use to win in this conflict is to simply have more mitochondria than their partner, for example, by increasing the size of their sex cells,” Andrew Pomiankowski said. “Strikingly, this might have been the impetus to evolve two sexes in the first place.” Larger sex cells – the future eggs – garnered an advantage in the battle over mitochondrial inheritance, simply by swamping smaller sex cells – the forerunners of sperm – that had fewer mitochondria to contribute.

Most biologists currently think that two sexes evolved through division of labor – a so-called “disruptive selection” theory. Large female sex cells can survive longer but cannot move much, while smaller sperm are fragile but move faster and can find more mating partners.

Our hypothesis on the origin of sexes, if true, adds a new angle to this origins story, tracing it back to an ancient conflict over mitochondrial inheritance. Females may have won this ancient battle by simply producing larger sex cells packed with mitochondria, ensuring that mitochondrial transmission is effectively one-sided (and reaping the long-term fitness benefits). But ultimately, as with all scientific hypotheses, this one will have to stand the test of thorough experimental verification.