Transitions, Transversions and Deletions in mitochondrial DNA and their relevance to Parkinsons, ALS/MND and Aging.
I aim to write this blog so that people don't need a detailed understanding of genetics to read it. I assume people know that genetics involves DNA being used to produce proteins. DNA is comprised of four nucleotides. Two of these are purines Adenine (A) and Guanine (G). The other two are pyrimidines Thymine (T) and Cytosine (C). They pair in two pairs A to T and G to C. Each pair is called a base pair. To produce a protein they are copied to mRNA (messenger RNA) which is then used by the ribosome to create proteins. There is DNA in the nucleus of the cell and there is also DNA in the mitochondria (the little chemical factories that generate ATP and other molecules used by the cell). There is a three base pair code (identifying which amino acid to use) used to convert DNA into protein (via mRNA). Interestingly the code is slightly different in the nucleus/ribosome to the mitochondria.
So far so good. DNA can be mutated where one nucleotide for some reason or other is changed to another. That, of course, would mean that the protein produced is the wrong one with a wrong amino acid replacing the correct one. There also deletions, but lets ignore those for the moment. An interesting thing about genetics is that it is part fault tolerant. If you compare it to a computer system it has aspects that are like a "check digit". A check digit for a bank account number (at least in the UK) means if you type in the number in the wrong order it can work out that there is a mistake simply by using the formula. This works for credit card numbers. They use the Luhn Algorithm. Similarly because genetics always has the same base pairs it can pick up minor errors in the base pair and refix the molecules. DNA also comes in two strands which also helps. If you want to read more about this there is a wikipedia page DNA Repair it is in the end quite complicated.
Any way, so when it comes to mutation of DNA there are three main types, transitions, transversions and deletions. Transition is where one of the pyrimidines is swapped for the other T → C, C → T, G → A or G → A. Transversion is where a pyrimidine is swapped for a purine A → C, A → T, G → C, G → T, C → A, C → G, T → A or T → G. Deletions is where a section of DNA is removed and the two ends join together making a shorter molecule of mtDNA. A high proportion of the mutations that are found in mtDNA are C → T and G → A.
Deletions are thought to be a result of oxidative stress, transversions are also thought to be as a result of oxidative stress, but transitions are subject to some debate. Some researchers believe that transitions all result from errors in replication by RNA Polymerase gamma (the enzyme that copies mtDNA). Other researchers believe that some transitions happen because of oxidative stress, but a material proportion happen from replication errors.
Mechanism of age-related accumulation of mitochondrial DNA mutations in human blood is an interesting paper recently which looked at the mitochondrial DNA in human blood from the UK biobank. An interesting chart from this paper is this one:
They say "Age-accumulating heteroplasmies show a mutational signature of replication error
Turning to heteroplasmic mtDNA SNVs, we observe a very strong pattern of mutation accrual after age 60 years (Figure 1). Despite the narrower age range (40-70 years versus 18-90 years in AoU), we find a similar accumulation in UKB (Extended Data Figure 5A). This accumulation occurred regardless of smoking status, however heteroplasmic SNVs were more abundant in smokers as described previously13 (Extended Data Figure 5B). We sought to elucidate the mechanism of this accumulation."
and
"Consistent with replication-related error, we observed a striking strand bias: both C>T and A>G variants occurred more frequently on the heavy strand relative to the light strand. In the nuclear genome, mutational strand bias can be seen in transcription-coupled nucleotide excision repair15. However, we observe similar bias regardless of the strand on which the gene is located (Figure 2D, Extended Data Figure 6D). The most commonly occurring variants had an NCG context (Extended Data Figures 7A, 8A), similar to that seen in a single-base substitution (SBS) pattern observed in cancers with nuclear DNA repair defects (SBS6)16. Many of most correlated SBS signatures were attributable to deamination and DNA repair defects within the nuclear genome (Extended Data Figure 7B, 8B), further suggestive of replication-related error. On the other hand, oxidative damage typically produce s age-increasing C>A transversions (and, to a lesser extent, A>C mutations) due to guanosine oxidation17–19."
Why does this matter in the real world
Finding the reason why mtDNA is mutated is really important for the function of cells. If the mitochondria become damaged this changes the way cells produce proteins (gene expression). I think it is the main cause of Aging and diseases of aging in which I include Parkinsons Disease and ALS/MND (because they result from accelerated damage to mitochondrial DNA in dopinamergic neurons and motor neurons respectively).
Somatic mitochondrial DNA mutations in early Parkinson's and incidental Lewy body disease is a paper that looks at mitochondrial DNA damage in people with early Parkinsons (as the disease progresses mtDNA damage gets worse and cells start dying).
The paper says: " In neurons, mean somatic mtDNA point mutation levels were more than 250 mutations/106 bp higher in early PD+ILBD compared to controls (p=0.0001) or late PD (p=0.0003), representing a 2-fold increase, but were similar in controls and late PD (difference of only ~42 mutations/106 bp, p=0.53) (Fig. 1A). We also examined levels of specific mutation subtypes, G→T or C→A transversions. These mutation subtypes are predicted to arise from mispairing induced by 8-hydroxy-2’deoxyguanosine (OH8dG), one of the most common products of oxidative damage to DNA,18 although they also may arise through other mechanisms. Levels of such potential oxidative stress mutations were over 100 mutations/106 bp higher in neurons from early PD+ILBD compared to controls (p < 0.0001) or late PD (p=0.0006), representing a 3-fold increase, but again were similar in controls and late PD (difference of only ~4 mutations/106 bp, p=0.89) (Figure 1B). Thus, in SN neurons, overall somatic mtDNA point mutation levels and levels of mutation subtypes that can arise from oxidative stress are both dramatically increased, but only in early PD+ILBD."
Another question is what the effect of the mutation is. A transition probably has the least effect, then a transversion and a deletion can have a major effect. In fact a deletion can cause major problems. Various species have been studied as to the prevalence of various mutations and generally transitions are found to be most common.
This is where heteroplasmy comes in. An individual mitochondrion has a number of copies of mtDNA. Heteroplasmy is where there are different versions of mtDNA in a mitochondrion or cell. There is in fact a common deletion (called oddly enough the "common deletion" discovered by Shoffner in 1989) that deletes 4,977 base pairs from positions 8,482–13,459. This removes six OxPhos genes and 5 tRNAs. This only cripples energy production, however, when a large number of copies of mtDNA have this deletion. Otherwise those proteins can be created from another copy of mtDNA. (A comprehensive overview of mitochondrial DNA 4977-bp deletion in cancer studies gives more information about the common deletion).
What is the conclusion The conclusion of this is ordinarily the process of gradual mtDNA mutation happens even without oxidative stress at a low level. This occurs through replication errors in RNA Pol gamma. However, oxidative stress will increase the speed of aging and major oxidiative stress that causes deletions will really create problems. In people with PD and ALS/MND it appears that the damage done in dopaminergic neurons and motor neurons respectively is so bad that it kills off some of the cells.
From a development clock perspective, therefore, there is actually a clock that does not require oxidative stress (although from an evolutionary perspective some oxidative stress will have selection effects).
Notes:
This paper has some transitions being oxidative damage related.
A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand
So far so good. DNA can be mutated where one nucleotide for some reason or other is changed to another. That, of course, would mean that the protein produced is the wrong one with a wrong amino acid replacing the correct one. There also deletions, but lets ignore those for the moment. An interesting thing about genetics is that it is part fault tolerant. If you compare it to a computer system it has aspects that are like a "check digit". A check digit for a bank account number (at least in the UK) means if you type in the number in the wrong order it can work out that there is a mistake simply by using the formula. This works for credit card numbers. They use the Luhn Algorithm. Similarly because genetics always has the same base pairs it can pick up minor errors in the base pair and refix the molecules. DNA also comes in two strands which also helps. If you want to read more about this there is a wikipedia page DNA Repair it is in the end quite complicated.
Any way, so when it comes to mutation of DNA there are three main types, transitions, transversions and deletions. Transition is where one of the pyrimidines is swapped for the other T → C, C → T, G → A or G → A. Transversion is where a pyrimidine is swapped for a purine A → C, A → T, G → C, G → T, C → A, C → G, T → A or T → G. Deletions is where a section of DNA is removed and the two ends join together making a shorter molecule of mtDNA. A high proportion of the mutations that are found in mtDNA are C → T and G → A.
Deletions are thought to be a result of oxidative stress, transversions are also thought to be as a result of oxidative stress, but transitions are subject to some debate. Some researchers believe that transitions all result from errors in replication by RNA Polymerase gamma (the enzyme that copies mtDNA). Other researchers believe that some transitions happen because of oxidative stress, but a material proportion happen from replication errors.
Mechanism of age-related accumulation of mitochondrial DNA mutations in human blood is an interesting paper recently which looked at the mitochondrial DNA in human blood from the UK biobank. An interesting chart from this paper is this one:
They say "Age-accumulating heteroplasmies show a mutational signature of replication error
Turning to heteroplasmic mtDNA SNVs, we observe a very strong pattern of mutation accrual after age 60 years (Figure 1). Despite the narrower age range (40-70 years versus 18-90 years in AoU), we find a similar accumulation in UKB (Extended Data Figure 5A). This accumulation occurred regardless of smoking status, however heteroplasmic SNVs were more abundant in smokers as described previously13 (Extended Data Figure 5B). We sought to elucidate the mechanism of this accumulation."
and
"Consistent with replication-related error, we observed a striking strand bias: both C>T and A>G variants occurred more frequently on the heavy strand relative to the light strand. In the nuclear genome, mutational strand bias can be seen in transcription-coupled nucleotide excision repair15. However, we observe similar bias regardless of the strand on which the gene is located (Figure 2D, Extended Data Figure 6D). The most commonly occurring variants had an NCG context (Extended Data Figures 7A, 8A), similar to that seen in a single-base substitution (SBS) pattern observed in cancers with nuclear DNA repair defects (SBS6)16. Many of most correlated SBS signatures were attributable to deamination and DNA repair defects within the nuclear genome (Extended Data Figure 7B, 8B), further suggestive of replication-related error. On the other hand, oxidative damage typically produce s age-increasing C>A transversions (and, to a lesser extent, A>C mutations) due to guanosine oxidation17–19."
Why does this matter in the real world
Finding the reason why mtDNA is mutated is really important for the function of cells. If the mitochondria become damaged this changes the way cells produce proteins (gene expression). I think it is the main cause of Aging and diseases of aging in which I include Parkinsons Disease and ALS/MND (because they result from accelerated damage to mitochondrial DNA in dopinamergic neurons and motor neurons respectively).
Somatic mitochondrial DNA mutations in early Parkinson's and incidental Lewy body disease is a paper that looks at mitochondrial DNA damage in people with early Parkinsons (as the disease progresses mtDNA damage gets worse and cells start dying).
The paper says: " In neurons, mean somatic mtDNA point mutation levels were more than 250 mutations/106 bp higher in early PD+ILBD compared to controls (p=0.0001) or late PD (p=0.0003), representing a 2-fold increase, but were similar in controls and late PD (difference of only ~42 mutations/106 bp, p=0.53) (Fig. 1A). We also examined levels of specific mutation subtypes, G→T or C→A transversions. These mutation subtypes are predicted to arise from mispairing induced by 8-hydroxy-2’deoxyguanosine (OH8dG), one of the most common products of oxidative damage to DNA,18 although they also may arise through other mechanisms. Levels of such potential oxidative stress mutations were over 100 mutations/106 bp higher in neurons from early PD+ILBD compared to controls (p < 0.0001) or late PD (p=0.0006), representing a 3-fold increase, but again were similar in controls and late PD (difference of only ~4 mutations/106 bp, p=0.89) (Figure 1B). Thus, in SN neurons, overall somatic mtDNA point mutation levels and levels of mutation subtypes that can arise from oxidative stress are both dramatically increased, but only in early PD+ILBD."
Another question is what the effect of the mutation is. A transition probably has the least effect, then a transversion and a deletion can have a major effect. In fact a deletion can cause major problems. Various species have been studied as to the prevalence of various mutations and generally transitions are found to be most common.
This is where heteroplasmy comes in. An individual mitochondrion has a number of copies of mtDNA. Heteroplasmy is where there are different versions of mtDNA in a mitochondrion or cell. There is in fact a common deletion (called oddly enough the "common deletion" discovered by Shoffner in 1989) that deletes 4,977 base pairs from positions 8,482–13,459. This removes six OxPhos genes and 5 tRNAs. This only cripples energy production, however, when a large number of copies of mtDNA have this deletion. Otherwise those proteins can be created from another copy of mtDNA. (A comprehensive overview of mitochondrial DNA 4977-bp deletion in cancer studies gives more information about the common deletion).
What is the conclusion The conclusion of this is ordinarily the process of gradual mtDNA mutation happens even without oxidative stress at a low level. This occurs through replication errors in RNA Pol gamma. However, oxidative stress will increase the speed of aging and major oxidiative stress that causes deletions will really create problems. In people with PD and ALS/MND it appears that the damage done in dopaminergic neurons and motor neurons respectively is so bad that it kills off some of the cells.
From a development clock perspective, therefore, there is actually a clock that does not require oxidative stress (although from an evolutionary perspective some oxidative stress will have selection effects).
Notes:
This paper has some transitions being oxidative damage related.
A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand
Comments