Recently another paper was produced which hinted at a link between mitochondrial DNA damage and aging. In fact I have been of the view for some time that the damage to mitochondrial DNA is what drives both aging and development at the lowest level. I have said this before, but thought a summary would be useful. It is worth, however, explaining a few terms first before going into the details of how this happens.
It is well known that animals (including people) are made of large number of cells. Within those cells there are little "organelles" called mitochondria that are used to convert nutrients into ATP (Adenosine Tri Phosphate) which is used by cells as a form of energy. There is a hypothesis that is generally believed to be true that this structure of cells arose from some bacteria going into old cells called archea as it created a form of symbiosis where the larger cells provided nutrients to the bacteria for the bacteria to process those. This is called Endosymbiosis with the mitochondrion being an Endosymbiont. Wikipedia have a useful page about this here:
https://en.wikipedia.org/wiki/Endosymbiont
It is also known that other molecules go in and out of the mitochondria via a number of transport proteins which are proteins which enable a particular molecule or set of molecules to pass through the wall of the mitochondrion. This means that there is a complicated system of communication between the mitochondria and the rest of the cells. In this article I am going to concentrate on Citrate which is transferred in and out of the mitochondria via a protein called the Citrate Carrier which has a gene called SLC25A1.
Citrate (which is the anion [negative ion] from Citric Acid) is particularly important not just because the main biochemical cycle in the mitochondria is called the "Citric Acid Cycle". It is also called the Krebs Cycle and the TCA cycle (TriCarboxylic Acid is another name for Citric Acid). When it leaves the mitochondrion it can be processed by an enzyme with the code ACLY which is called ATP Citrate Lyase. This converts citrate (plus other things) into acetyl-CoA (and Oxaloacetate). Acetyl-CoA is thought of as being a metabolite that has a long history and it is used for a large number of things in the area outside the mitochondria called the Cytosol.
One of the things Acetyl-CoA is used for is to add an acetyl Group to a protein. This is called acetylation.
Acetylation is important because it changes how other molecules behave. In particular when the "histone" which is a protein to which DNA is attached is acetylated it has the effect of opening up the DNA. This is helpful for an enzyme called RNA Polymerase II which can then more easily read the DNA and produce mRNA (from which at a later stage proteins are produced).
Another thing that is affected by acetylation is the process of mRNA Splicing. It is also well known that cells don't necessarily produce exactly the same protein from the same genes. There is a process where parts of a gene are transcribed (the process of reading it and creating mRNA) and then spliced together in various different ways. Hence it is possible for different proteins to be produced in different circumstances.
This is particularly important when it comes to aging and development. It has been known for some time that the splicing decisions are dependent upon the levels of acetyl-CoA (and as a consequence levels of acetylation) in the nucleus (which of course depends upon acetyl-CoA produced in the cytosol). It is also possible now to study the splicing in particular cells and it is becoming clear that development is often initially driven by splicing. If we consider for example puberty which is driven by the hypothalamus-pituitary-gonadal (HPG) axis. This involves a hormone called gonadotropin-releasing hormone. The release of this hormone is affected by a large number of things. One of those things, however, is a hormone called kisspeptin. This is produced from the KISS1 gene. This gene is affected by mRNA splicing which influences how other parts of the body respond to the hormone. In a similar manner the KISS1R gene, which is the gene for the kisspeptin receptor, is also affected by mRNA splicing.
Alternative Splicing Dynamics of the Hypothalamus–Pituitary–Ovary Axis During Pubertal Transition in Gilts is a paper that looks at the links between splicing and puberty in pigs. They don't conclude that the timing of puberty in pigs is definitely a result of splicing, but it is seen as something that is likely to be a factor in the timing.
Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases is one of a number of papers that have looked at the links between splicing and age related diseases. It concludes "We find that genome-wide splicing profile is a better predictor of biological age than the gene and transcript expression profiles, and furthermore, age-associated splicing provides additional independent contribution to age-associated complex diseases."
However, not all age related diseases are caused by splicing issues. Some such as Osteoporosis are caused by cells failing to differentiate. In the case of Osteoporosis we have to start by understanding that the state of the skeleton is normally in a dynamic equilibrium. Cells called osteoclasts are removing bone, cells called osteoblasts are rebuilding bone. However, as people get older the stem cells that should create the builders (osteoblasts) fail to differentiate so the bone tissue is broken down by the osteoclasts, but not fully replaced. Hence bones break.
Interestingly a few years ago it was discovered that this was because there was too little citrate coming out of the mitochondria. There are a number of aging diseases which are caused by the failure to differentiate. It is interesting, therefore, that both splicing changes and failure to differentiate are caused by too little citrate coming out of the mitochondria.
So why does this happen?
First we need to consider what the influences are on citrate coming out of the mitochondria. It comes out via the citrate carrier, so if there are not enough citrate carriers in the mitochondrial membrane wall you won't get enough citrate leaving. The second big influence is how much citrate is stored in the mitochondria. Citrate is created from pyruvate and oxaloacetate. The oxalocetate is part of either the main citric acid cycle or the non-canonical cycle (that which passes through the citrate carrier) so there won't be a shortage of oxaolacetate. Hence the main cause is the rate of pyruvate influx.
We now need to look at bit more at the structure of the mitochondria. Without going into the details there is a structure of five complexes each made of a large number of units called the electron transport chain (ETC). When a mitochondrion is functioning properly the ETC develops a strong electrical field at the edge of the mitochondrion. This is mainly at the inner wall (inner mitochondrial membrane) of the mitochondrion. Although this is only measured in milliVolts (thousandths of a volt) it is over a very short distance so the field is quite strong given the distance. This is known as the Mitochondrial Membrane Potential and is given the symbol ΔΨM.
Although Pyruvate is neutral and therefore not subject directly to the electrical force it is subjected to the proton gradient because it needs protons to come into the mitochondria via its own transport protein. The proton gradient is maintained by the Mitochondrial Membrane Potential.
So we now have two things that can affect splicing and differentiation. A) The Mitochondrial Membrane Potential and B) The number of citrate carriers in the mitochondrial membrane.
I will come to B) later as it seems quite clear that A) is the most important. The Mitochondrial Membrane Potential is an indicator of how efficient the mitochondria are. A higher potential means a higher efficiency. The efficiency can be measured in the ATP/O ratio which is the number of units of ATP produced for each unit of Oxygen consumed. This is where the detail of the operation of the ETC comes in. I am going to gloss over this for now. However, let us start with the idea that there are a large number of proteins that make up the five complexes of the ETC. If the proteins are changed then things may work better, and may be less efficient. If the proteins are changed too much then it may not work at all. Hence small changes to the proteins are likely to make small changes to the efficiency of the ETC. It seems obvious that random changes are more likely to make things less efficient than more. (With the knock on effects on the rest of the system).
The DNA code for the proteins in the ETC is actually stored in two places. A lot of the DNA is stored in the nucleus of the cell. This is a bit of a nuisance for the cell when a protein needs replacing as it has to be transported from the nucleus to the mitochondrion. Some of the DNA, however, is still stored in the mitochondrion. This is known as mitochondrial DNA or mtDNA. There a number of differences between mtDNA and nucDNA. Interestingly the code used to change the mtDNA into proteins is different to nucDNA, but that is not that important a difference. More importantly mtDNA is stored in a circle and is not stored on a histone. The lack of a histone makes it much more vulnerable to damage from wandering reactive molecules. Often there is more than one copy of mtDNA in an individual mitochondrion. Also mtDNA is replicated as part of the mitochondrial life cycle. When an egg is fertilised the paternal mtDNA is lost (either it is destroyed or there is so little paternal mtDNA compared to material mtDNA that it is insignificant).
The issue, therefore, is that if there are wandering reactive molecules (Reactive Oxygen Species, Reactive Nitrogen Species, Free Radicals (both ROS and RNS)) then there is a risk that the mtDNA will damaged and at times even if the DNA can be repaired it ends up mutated and the mitochondria become less efficient. They therefore have a lower Mitochondrial Membrane Potential and the gene expression changes (either RNA splicing is different or cells don't differentiate). The basic problem, although it could be described as a feature rather than a bug, is that Complex 1 to a great extent and also Complex 3 of the ETC generate a lot of Reactive Oxygen Species. Hence as the mitochondria go about their ordinary daily business of generating energy they do damage to their own mtDNA which makes them less efficient.
Interestingly in mammallian eggs (oocytes) complex 1 is inhibited or not expressed and therefore much less ROS is generated and the egg mitochondria remain in a better state. As eggs are generally created when the mother is herself an embryo the mitochondria in them have not had enough activity to be damaged. Because there is a selective process when an egg is created which limits the range of mtDNA to a small number of variations in mtDNA (called the bottleneck) the chances are that the mitochondria in eggs are in a good state. If they are not then one would expect any fertilised egg to miscarry at an early stage.
So this is it. Development and Aging is controlled primarily by the state of mitochondrial DNA.
The second control relates to the presence of SLC25A1 in the mitochondrial membrane. (B - above) Interestingly this protein is dependent on Nuclear Factor Kappa B which is a sign of inflammation. That is inhibited by Interleukin-10. IL-10 is part of the Senescence Associated Secretary Phenotype which is a mixture of cytokines secreted by senescent cells. Hence it would be reasonable to see that as a secondary driver of aging which both creates more cells which fail to differentiate, but also more generally reduces cytosolic acetyl-CoA levels causing additional aging.
There is in fact a small amount of research that shows that IL-10 can cause senescence. This is research that would be difficult to get into a journal as it goes against the conventional wisdom as IL-10 is anti-inflammatory.
Obviously the first question anyone would ask given the above is what can be done about this. The answer is lots, but that is a topic for another day.
Some papers if people want to read up on this
Cryptic mitochondrial DNA mutations coincide with mid-late life and are pathophysiologically informative in single cells across tissues and species
Mitochondrial ROS-Modulated mtDNA: A Potential Target for Cardiac Aging
Mechanisms linking mtDNA damage and aging
It is well known that animals (including people) are made of large number of cells. Within those cells there are little "organelles" called mitochondria that are used to convert nutrients into ATP (Adenosine Tri Phosphate) which is used by cells as a form of energy. There is a hypothesis that is generally believed to be true that this structure of cells arose from some bacteria going into old cells called archea as it created a form of symbiosis where the larger cells provided nutrients to the bacteria for the bacteria to process those. This is called Endosymbiosis with the mitochondrion being an Endosymbiont. Wikipedia have a useful page about this here:
https://en.wikipedia.org/wiki/Endosymbiont
It is also known that other molecules go in and out of the mitochondria via a number of transport proteins which are proteins which enable a particular molecule or set of molecules to pass through the wall of the mitochondrion. This means that there is a complicated system of communication between the mitochondria and the rest of the cells. In this article I am going to concentrate on Citrate which is transferred in and out of the mitochondria via a protein called the Citrate Carrier which has a gene called SLC25A1.
Citrate (which is the anion [negative ion] from Citric Acid) is particularly important not just because the main biochemical cycle in the mitochondria is called the "Citric Acid Cycle". It is also called the Krebs Cycle and the TCA cycle (TriCarboxylic Acid is another name for Citric Acid). When it leaves the mitochondrion it can be processed by an enzyme with the code ACLY which is called ATP Citrate Lyase. This converts citrate (plus other things) into acetyl-CoA (and Oxaloacetate). Acetyl-CoA is thought of as being a metabolite that has a long history and it is used for a large number of things in the area outside the mitochondria called the Cytosol.
One of the things Acetyl-CoA is used for is to add an acetyl Group to a protein. This is called acetylation.
Acetylation is important because it changes how other molecules behave. In particular when the "histone" which is a protein to which DNA is attached is acetylated it has the effect of opening up the DNA. This is helpful for an enzyme called RNA Polymerase II which can then more easily read the DNA and produce mRNA (from which at a later stage proteins are produced).
Another thing that is affected by acetylation is the process of mRNA Splicing. It is also well known that cells don't necessarily produce exactly the same protein from the same genes. There is a process where parts of a gene are transcribed (the process of reading it and creating mRNA) and then spliced together in various different ways. Hence it is possible for different proteins to be produced in different circumstances.
This is particularly important when it comes to aging and development. It has been known for some time that the splicing decisions are dependent upon the levels of acetyl-CoA (and as a consequence levels of acetylation) in the nucleus (which of course depends upon acetyl-CoA produced in the cytosol). It is also possible now to study the splicing in particular cells and it is becoming clear that development is often initially driven by splicing. If we consider for example puberty which is driven by the hypothalamus-pituitary-gonadal (HPG) axis. This involves a hormone called gonadotropin-releasing hormone. The release of this hormone is affected by a large number of things. One of those things, however, is a hormone called kisspeptin. This is produced from the KISS1 gene. This gene is affected by mRNA splicing which influences how other parts of the body respond to the hormone. In a similar manner the KISS1R gene, which is the gene for the kisspeptin receptor, is also affected by mRNA splicing.
Alternative Splicing Dynamics of the Hypothalamus–Pituitary–Ovary Axis During Pubertal Transition in Gilts is a paper that looks at the links between splicing and puberty in pigs. They don't conclude that the timing of puberty in pigs is definitely a result of splicing, but it is seen as something that is likely to be a factor in the timing.
Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases is one of a number of papers that have looked at the links between splicing and age related diseases. It concludes "We find that genome-wide splicing profile is a better predictor of biological age than the gene and transcript expression profiles, and furthermore, age-associated splicing provides additional independent contribution to age-associated complex diseases."
However, not all age related diseases are caused by splicing issues. Some such as Osteoporosis are caused by cells failing to differentiate. In the case of Osteoporosis we have to start by understanding that the state of the skeleton is normally in a dynamic equilibrium. Cells called osteoclasts are removing bone, cells called osteoblasts are rebuilding bone. However, as people get older the stem cells that should create the builders (osteoblasts) fail to differentiate so the bone tissue is broken down by the osteoclasts, but not fully replaced. Hence bones break.
Interestingly a few years ago it was discovered that this was because there was too little citrate coming out of the mitochondria. There are a number of aging diseases which are caused by the failure to differentiate. It is interesting, therefore, that both splicing changes and failure to differentiate are caused by too little citrate coming out of the mitochondria.
So why does this happen?
First we need to consider what the influences are on citrate coming out of the mitochondria. It comes out via the citrate carrier, so if there are not enough citrate carriers in the mitochondrial membrane wall you won't get enough citrate leaving. The second big influence is how much citrate is stored in the mitochondria. Citrate is created from pyruvate and oxaloacetate. The oxalocetate is part of either the main citric acid cycle or the non-canonical cycle (that which passes through the citrate carrier) so there won't be a shortage of oxaolacetate. Hence the main cause is the rate of pyruvate influx.
We now need to look at bit more at the structure of the mitochondria. Without going into the details there is a structure of five complexes each made of a large number of units called the electron transport chain (ETC). When a mitochondrion is functioning properly the ETC develops a strong electrical field at the edge of the mitochondrion. This is mainly at the inner wall (inner mitochondrial membrane) of the mitochondrion. Although this is only measured in milliVolts (thousandths of a volt) it is over a very short distance so the field is quite strong given the distance. This is known as the Mitochondrial Membrane Potential and is given the symbol ΔΨM.
Although Pyruvate is neutral and therefore not subject directly to the electrical force it is subjected to the proton gradient because it needs protons to come into the mitochondria via its own transport protein. The proton gradient is maintained by the Mitochondrial Membrane Potential.
So we now have two things that can affect splicing and differentiation. A) The Mitochondrial Membrane Potential and B) The number of citrate carriers in the mitochondrial membrane.
I will come to B) later as it seems quite clear that A) is the most important. The Mitochondrial Membrane Potential is an indicator of how efficient the mitochondria are. A higher potential means a higher efficiency. The efficiency can be measured in the ATP/O ratio which is the number of units of ATP produced for each unit of Oxygen consumed. This is where the detail of the operation of the ETC comes in. I am going to gloss over this for now. However, let us start with the idea that there are a large number of proteins that make up the five complexes of the ETC. If the proteins are changed then things may work better, and may be less efficient. If the proteins are changed too much then it may not work at all. Hence small changes to the proteins are likely to make small changes to the efficiency of the ETC. It seems obvious that random changes are more likely to make things less efficient than more. (With the knock on effects on the rest of the system).
The DNA code for the proteins in the ETC is actually stored in two places. A lot of the DNA is stored in the nucleus of the cell. This is a bit of a nuisance for the cell when a protein needs replacing as it has to be transported from the nucleus to the mitochondrion. Some of the DNA, however, is still stored in the mitochondrion. This is known as mitochondrial DNA or mtDNA. There a number of differences between mtDNA and nucDNA. Interestingly the code used to change the mtDNA into proteins is different to nucDNA, but that is not that important a difference. More importantly mtDNA is stored in a circle and is not stored on a histone. The lack of a histone makes it much more vulnerable to damage from wandering reactive molecules. Often there is more than one copy of mtDNA in an individual mitochondrion. Also mtDNA is replicated as part of the mitochondrial life cycle. When an egg is fertilised the paternal mtDNA is lost (either it is destroyed or there is so little paternal mtDNA compared to material mtDNA that it is insignificant).
The issue, therefore, is that if there are wandering reactive molecules (Reactive Oxygen Species, Reactive Nitrogen Species, Free Radicals (both ROS and RNS)) then there is a risk that the mtDNA will damaged and at times even if the DNA can be repaired it ends up mutated and the mitochondria become less efficient. They therefore have a lower Mitochondrial Membrane Potential and the gene expression changes (either RNA splicing is different or cells don't differentiate). The basic problem, although it could be described as a feature rather than a bug, is that Complex 1 to a great extent and also Complex 3 of the ETC generate a lot of Reactive Oxygen Species. Hence as the mitochondria go about their ordinary daily business of generating energy they do damage to their own mtDNA which makes them less efficient.
Interestingly in mammallian eggs (oocytes) complex 1 is inhibited or not expressed and therefore much less ROS is generated and the egg mitochondria remain in a better state. As eggs are generally created when the mother is herself an embryo the mitochondria in them have not had enough activity to be damaged. Because there is a selective process when an egg is created which limits the range of mtDNA to a small number of variations in mtDNA (called the bottleneck) the chances are that the mitochondria in eggs are in a good state. If they are not then one would expect any fertilised egg to miscarry at an early stage.
So this is it. Development and Aging is controlled primarily by the state of mitochondrial DNA.
The second control relates to the presence of SLC25A1 in the mitochondrial membrane. (B - above) Interestingly this protein is dependent on Nuclear Factor Kappa B which is a sign of inflammation. That is inhibited by Interleukin-10. IL-10 is part of the Senescence Associated Secretary Phenotype which is a mixture of cytokines secreted by senescent cells. Hence it would be reasonable to see that as a secondary driver of aging which both creates more cells which fail to differentiate, but also more generally reduces cytosolic acetyl-CoA levels causing additional aging.
There is in fact a small amount of research that shows that IL-10 can cause senescence. This is research that would be difficult to get into a journal as it goes against the conventional wisdom as IL-10 is anti-inflammatory.
Obviously the first question anyone would ask given the above is what can be done about this. The answer is lots, but that is a topic for another day.
Some papers if people want to read up on this
Cryptic mitochondrial DNA mutations coincide with mid-late life and are pathophysiologically informative in single cells across tissues and species
Mitochondrial ROS-Modulated mtDNA: A Potential Target for Cardiac Aging
Mechanisms linking mtDNA damage and aging
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