Mitochondrial dysfunction and protein misfolding in age-related neurodegeneration

Mitochondrial Diseases

A gene is basically a one dimension sequence of nucleotides that signals for the production of a protein. (Reynaud, 2010) The protein itself is merely a sequence of amino acids arranged in a specific manner. The sequence of the gene is linear and so is the sequence of the protein. DNA, which is a common term heard now and then is merely a collective term for all the genes of the body. The mechanism by which genes on the DNA work its action and are expressed in the body is known as translation. (Reynaud, 2010) Through translation, the genes come out as proteins and thus do specific actions in the body. The amino acid sequence mentioned earlier basically is a blue print that tells how the protein is going to be made and what specific function it will do.

The genetic material that we have is present in every single cell of the body. Regardless of which cell it is, the DNA and the genes are always present t in it. The proteins that the gens make carry out the required acts that a person needs to do in order to live and grow. Along with the bodily functions and actions, it is genes that that determine how we look, the way we act and how are body functions two. Even a little kid knows that he got half his genes from the mother and half from the father. However, it is not only looks that our mother and father decide. Their genes and consequently our genes also decide whether all the functions in our body will be normal or not. Some errors or defects in a genetic sequence can carry on for generations and thus give rise to inherited diseases. A mutation in the simplest forms is an n error or a defect in the genetic sequence of a person. Some mutations may go unnoticed and not produce any harmful effects. On the other hand, mutations may alter the production of certain proteins that go on to affect our body negatively. These negative effects then cumulate and present in the form of inherited disorders that are so common.

Thesis

Age and Age related diseases have been linked to the declining function of the mitochondria of cells in the body. Aging is a natural process and the senescence has been linked to processes like DNA methylation, telomerase shortening and the lastly the damage done by reactive oxygen species made by the mitochondria. (Schapira, 2012) The mitochondrial dysfunction can lead to production of ROS that damages cells like the neurons in Substantia Niagara in the brain and lead to diseases like Parkinson's. Also, the mitochondrial dysfunction causes the production and further accumulation of abnormally folded proteins that causes more degeneration. These effects are observed in other organs and systems and cause disease like Alzheimer's and diabetes as well. With the ongoing research on the link between mitochondrial DNA mutations and degenerative disorders, much is being done to figure out diagnosis, treatment and prevention of disorders like Parkinson's disease.

Protein Folding Diseases

The information required for proteins to fold correctly resides in the amino acid sequence. According to Levinthals Paradox, the proteins fold very fast into their most stable form because all the amino acids interact locally. (Reynaud, 2010) These interactions and the limited space thus make the proteins fold into the proper format. The proteins that have a difficult time folding into their native state, take help from chaperone molecules that make sure that the proper format is achieved. Ron Lackey mentioned the term chaperone when he found out that nucleoplasmin is bale to bind to histones and thus ensure the interaction between histones and DNA doesn't go haywire. That is to say that nuceloplasmin functioned as a chaperone and thus ensures that no inappropriate interactions take place. (Reynaud, 2010) The chaperones are necessary in some instances so the proteins don't go away from their native state and thus alter their own three dimensional structure. The three dimensional structure is crucial in determining how a protein will at in the body.

For most of the proteins, the most apparent structural motif is the structural confirmation that is popular as alpha helix. Whenever a protein misfolds or in simpler terms becomes toxic, it takes on the beta form. Misfolding basically occurs when a protein goes about a different pathway for folding or it follows an energy minimizing funnel. (Reynaud 2010) The toxic or the misfiled form of the protein then goes on to interact with the normal proteins and make them turn into a toxic state. That is when the proteins become infectious and are known as a prion. These prions are known as infectious because neither are they detected by the cells protective mechanisms nor removed by ultra violet radiation.

Protein misfolding and the way it is incorporated into membranes is an important factor in causing diseases. There are many diseases that are due to mutation in the a1 anti-trypsin and neuroserpin that give rise to protein misfolding. (Appella & Johansson, 2011) So why exactly is protein folding a bad thing? Surely proteins go on to carry important functions and one might say that if they're misfiled, they just won't do the function. The deposition of proteins in abnormal places can give rise to derangements in the normal functioning of the body. A common type of prion is one that is filled with beta pleated sheets and can give rise to amyloids that can be very harmful for the body. (Norrby 2011) Prion related disorders were proven when a prion infected protein rich food was used to feed the cattle. This led to a pandemic of bovine spongiform brain disorder which was acquired when anyone consumed the infected meat. (Norrby 2011) The amyloid formation that is created by protein misfolding gives rise to many diseases like type 2 diabetes and Alzheimer's disease. (Appella & Johansson, 2011) Many studies and reviews have been done to highlight how the protein aggregation and deposition is all because of misfolding. T The deposition is harmful and so is the interaction that the misfiled proteins go on to have with the membrane of different cells in the body. (Appella & Johansson, 2011)

A lot of the neurodegenerative diseases known are known to be because of abnormal accumulation of portion aggregates. It is seen that when these proteins deposits, brain function gets damaged at a cellular and at the synapse level as well. A suggestion that is sent forward is that increased stress on the endoplasmic reticulum of a cell is a leading cause of dysfunction in the long run. (Matus, Glimcher & Hetz, 2011)

There is still a lot of uncertainty in determining what the reason for protein misfolding is. One speculation is that sometimes same sort of protein chains known as homologous proteins are present in the body with a set blueprint on how exactly they will fold. When one of the protein folds, the other proteins similar to it fold in the same manner and thus make aggregates that have detrimental effects. (Norrby 2011) The aforementioned mechanism has thought to be one of the leading causes of degenerative disorders. A second speculation could be that certain amino acids are prone to being pathogenic. The amino acids are present in a sequence that can lead to them misfolding and thus producing diseases.

How exactly did the idea about protein causes diseases come out forward? The Creutzfeldt-Jakob disease was discovered by two German neurpathologists in 1920s. (Norrby 2011) This disease is characterized by slow destruction of the neural tissue known as spongiform encephalopathy. The incidence of this disease kept increasing yet no one knows what exactly caused the disease. More than 80% of the cases of this disease were sporadic and only ten percent were familial. (Norrby 2011)

There were many links seen between CJD, scrapies in sheep and Kuru in the Stone Age Fore people. Kuru was a serious neurological disease that was said to be caused by an infectious agent. A major route of infection of this disease was due to the ritual of cannibalism that was taken by the Fore people. When someone died, their body would be taken for the funeral meal and the women and children for the brain. The central nervous system had the biggest concentration of this disease thus it spread to women and children. CJD was a more established and reformed form of Kuru but the cause still could not be found. In the 1970s when Gajdusek examined the brain tissue of infected hamster, he tried to isolate what the causing mechanism was. The scientist initially thought it to be virus yet the results revealed something more pure. (Norrby 2011) Since he could not discover any nucleic acid, he went on to name it a prion. This word was an amalgamation of both an infectious and a protein like agent. Further studies into the agent gave the discovery that this protein was created by a gene inside the person's own body. This explains why there went any inflammatory response to the infection. Since the body's genes itself made the disease, there was no host response present. (Norrby 2011)

The misfolded proteins once made should be destroyed by the detective machinery inside the cell, however when these proteins increase in number, the cell cannot work out its investigative functions anymore. Protein misfolding can either occur spontaneously or by a mutation in the gene. Sickle cell anemia is a disorder that is inherited and leads to the improper folding of the proteins that make up hemoglobin. (Botelho & Lupi, 2008)

The amyloid diseases consist of Parkinson's, Alzheimer, type II and other cutaneous or systemic amyloidosis. The diseases that are caused because of the prions are not considered amyloid disease in the general term because they only represent a certain category of protein misfolding disorders. Some forms of amyloidosis are the ones that are transmitted from generation to generation. The mutation in the genetic code leads to abnormal proteins that lead to their aggregation and thus amyloid pathologies in the long run. The amyloidosis problems can further be divided into systemic and cutaneous diseases depending on which of the proteins become amyloid-genic. (Botelho & Lupi, 2008) Prion diseases differ from amyloidic because of them being localized to the central nervous system and also because of the way they are transmitted. When talking about amyloidosis, usually one protein becomes the causative factor and then goes to deposit in certain tissues. IT is the mere deposition there that causes disorders then. For instance, the B. amyloid protein goes on to collect in the CNS and leads to Alzheimer. Similarly, the a-synuclein protein collects in the CNS and the dopaminergic centers and goes to cause Parkinson's. (Botelho & Lupi, 2008)

Parkinson's disease

Parkinson's disease is one of the most common neurodegenerative disorder that affects about 2% of the above 60 population all over the world.(Licker et al., 2009) The current epidemiological research has stated that the prevalence of this disease is expected to increase and double in the coming twenty years. Seeing how this is a burden on the new world and a challenge that is expected, a lot of research is being done to figure what exactly causes Parkinson's disease. Surely, if we know the cause, the therapeutic techniques will be better understood as well.

Parkinson's disease has been a subject of research since a long time. There have been attempts to see who is susceptible to the disease, how it progresses and what the etiologic factors behind it are. The common cause of the Parkinson's disease is said to be an amalgamation of environmental and genetic factors. The mechanisms that are involved in this are mitochondrial dysfunction, oxidative stress, iron deposition, and inflammation. (Licker, Kovari, Hochstrasser & Burkhard, 2009) A lot data is pointing toward the aggregation of an abnormal form of neuronal protein a-synuclein that leads to degeneration in the long run. (Licker et al., 2009)

Parkinson's disease is a disease that produces a distinct and asymmetric combination of resting tremors and rigidity of the body. The person affected has difficulty initiating and stopping movement and isn't able to carry out simple tasks like writing or sketching. The person also experiences postural instability and since the disease is of a progressive nature, it keeps getting worse as it proceeds. (Licker et al., 2009)

The simplest pathology discovered about PD is that there is a loss of dopamine secreting Substantia Niagara neurons in the pons and midbrain (Licker et al., 2009) It was revealed that the neurons that did stay showed inclusions that are known as Lewy bodies or pale bodies. The Lewy bodies (Lbs) or the Lewy neuritis (Lns) when contained in the neuronal process is seen to consist of a-synuclein. The aggregation of these proteins continues to increase in a caudal-rostral manner as the disease progresses in its course. (Licker et al., 2009) The inclusions start of from the dorsal motor nucleus of the vagus nerve in the brainstem then keep going anteriorly towards the olfactory bulb and the anterior olfactory nucleus. (Licker et al., 2009)

The argument for this is that the a-SYN inclusions are also present in other neurological conditions as well. These conditions are collectively known as "alpha-synucleinopathies" which also have disease multiple system atrophy, Alzheimer's disease and with brain iron accumulation type 1. (Licker et al., 2009)

The protein folding that does occur is not a random but seems to occur very specifically. There are certain homologous proteins that seem to clump thus leading to abnormalities. Normally the ubiquitin-proteasome system (UPS) and peptidases go on to destroy the abnormal proteins. When the amount of aggregated proteins outruns the capacity of UPS, there is formation of soluble monomers and oligomers and eventually the formation of Lewis bodies in PD. (Licker et al., 2009) The collection of Lbs and LNs then lead to disrupt the normal cellular processes like synaptic plasticity, transmission from neuron to neuron and axonal transport. The dysfunction of the UPS has been proposed to be a major factor in causing the pathogenesis of PD disease. (Licker et al., 2009)

Mitochondrial Diseases

We have covered why protein misfolding can lead to disorders all over the body and especially in the brain. Our attention is now turned to Mitochondria and the important role they have in cellular energy and cell death. PD along with many other diseases is an example when certain cells lose their function. In the simplest terms, if mitochondria provides the energy for cells and controls their death, then surely it has a link to the many degenerative disorders known today. Mitochondrial diseases that are carried from generations could be due to DNA in the mitochondria or genes that code for the mitochondrial proteins. (Schapira, 2012) Optic neuropathy and type 2 diabetes are examples of tissue specific mitochondrial disorders.

As mentioned earlier mitochondrial diseases can result from point mutations to the DNA, alterations in the cellular DNA and free radical mediated destruction. (Schapira, 2012) Mitochondrial fission and fusion is an important mechanism by which the organelle is transported to do its many functions. Inhibition of the fission by destruction of dynamin-1-like protein can cause an augmentation in the amount of mutant mitochondrial DNA (mtDNA). The mtDNA can then be further linked to lactic acidosis, encephalomyopathy and stroke like symptoms. (Schapira, 2012) PTEN induced putative kinase 1 (PINK 1) and Parkin has a crucial role in the mitophagy pathway. (Schapira, 2012) Parkin is an enzyme that helps in the movement of products from the cytoplasm to the mitochondria. Pink1 phosphorylates the aforementioned molecule and gets the job done. Mutations in the gens for these two proteins are prominent in causing PD as discussed later in the paper.

Along with mutations and oxidative damage, the functions of mitochondria are known to decrease since age as well. This could be due to the accumulation of ROS in the body that keeps on affecting the mitochondria. Deletions and mutations are seen normally in mtDNA as a person ages. (Schapira, 2012)

Single Deletions

Single deletions of mtDNA were the first genetic defects to be linked with human mitochondrial disorders. (Pitceathly, Rahman & Hanna, 2012) It was revealed that out of the patients diagnosed with mtDNA linked disease, single deletions were the causative agent behind 25% of all the diseases. Single deletions are considered sporadic and thus have no link of inheritance or the defected gene being transferred over many generations. (Pitceathly et al., 2012) The exact mechanism of the replication of mtDNA is not known yet most of the single cell deletions do take place while the DNA is replicating. (Pitceathly et al., 2012) Most of the genetic defects linked to the mitochondria are the ones that results in the loss of any one of the respiratory chain agent. Some of the clinical disorders associated with single deletions are Kearns-Sayre syndrome, Pearson marrow-pancreas syndrome, myopathies, deafness and diabetes. (Pitceathly et al., 2012)

Mitochondrial DNA & (tRNA & mRNA) Mutations

Even though it a challenge to diagnose and establish a disease belong to mitochondrial origin, there should be work on treating the disease as well. The satellite cells are present between the basal lamina and the muscle fiber. These are important in diagnosing a disease of this origin. Other ways of figuring out if someone has this disease is amniocentesis, chronic villus biopsy and polar body. (Taylor & Turnbull, 2005)

When it comes to mitochondrial DNA, there is homoplasmy which means all the copies of the mitochondrial genome are the same. On the other hand, there is heteroplasmy in which there are two or three forms of the mitochondrial mutations. There are mutations that affect all the copies of the genome and are obviously more severe. In the case of heteroplasmy mutations, there is a threshold level of mutation that has to be present in order for the symptoms to appear. (Taylor & Turnbull, 2005) Mitochondrial mutations are transmitted from mothers to their offspring thus fathers don't have to fret that they can infect their child. (Taylor & Turnbull, 2005)

The 16.6 kb worth of human mitochondrial genomic has a total of thirty seven genes. Out of all the 37, only 13 code for structural proteins. (Dunn, Cannon, Irwin & Carl, 2012) Most of the proteins that are coded for are actually complexes essential to the oxidative function in the mitochondria. There are 22 Trnas and 2 Rrnas that are coded by the mitochondrial DNA. (Dunn et al., 2012) Out of the many studies done on mutations of the mitochondria, it was revealed that they are crucial in causing neurological and myopathy diseases, (Dunn et al., 2012)

Since a person cannot phenotypically discern that a mutation is of mitochondrial origin, animals were used to see how alteration in genes led to mutations. Methods used to test mitochondrial DNA, RNA and MRNA mutation were Somatic cell nuclear transfer, allotropic expression, Polymerase gamma mutations, Direct injection of mitochondria into embryos, Cytoplasmic hybrids, Rho-zero cells, trans mitochondrial mice, and Xenomitochondrial modeling. (Dunn et al., 2012)

Mitochondrial Medicine

Aging is a natural phenomenon yet there is been a close correlation of aging, age related diseases and mitochondrial dysfunction. Mitochondrial dysfunction has been linked to severe diseases like Alzheimer, Diabetes, PD and many others. Out of all the theories presented about mitochondria, the fact that is linked to aging and death is a one that is accepted till now. (Mao et al., 2012) It was mentioned earlier that most of the e single deletions mutations occurred during replication. Another theory proposed is that the mutations occur during the repairing of damaged manna. (Mao et al., 2012) The study conducted on the rhesus monkey was to figure out the link between mtDNA and effects of aging on monkeys. The blood, brain and the buffy coat of the monkeys was analyzed via using amplification and PCR techniques. These results revealed that mutated DNA was increased till a significant amount in aged monkeys as opposed to young monkeys. (Mao et al., 2012) The age dependent changes in the DNA in mitochondria can be utilized to target beneficial therapeutics against diseases caused by mitochondrial damage. It was proposed that this increase in mutated DNA could be due to declining mitochondrial function as the monkey ages. (Mao et al., 2012)This study thus builds up on the previous one discussed in the paper that increased oxidative stress as the person ages leads to more mitochondrial damage

Management of Mitochondrial Disease

The fact that mitochondrial dysfunction has been linked to PD has caused this issue to receive a lot of attention in designing approaches to fix the underlying cause. There has been therapeutic management approaches designed both on the drug level and the gene level as well. PD is a result of destruction of dopamine secreting neurons and other forms of cellular damage as well. Since neurons have such a high demand for energy, they are prone to mitochondripathies. (Pienaar&Chinnery, 2012) The early therapeutic alterations were aimed to fix the dopaminergic system that was dysfunctioning and thus correcting the motor problems. These drug however have had many side effects and led to other motor and psychiatric effects (Pienaar & Chinnery, 2012). Creatinine was an approach considered to stop or slow the progression of neuronal damage in PD. Some studies show that chronic Creatinine supplemental relevantly improved the survival of the dopamine secreting neurons in an animal trial of PD. (Pienaar & Chinnery, 2012)

Another approach that proved to be beneficial was the lowering of cholesterol levels in order to protect the neurons from further damage. Different studies have been done to see whether the use HMG CoA inhibitors (Statins) decrease the progression of PD. Huang et al. were the first ones to take out evidence that statin treatment had a neuroprotective effect on the treatment of PD. (Pienaar&Chinnery, 2012) Along with lowering serum cholesterol levels, lowering serum glucose has also been proved to be of benefit in treatment of mitochondrial dysfunction. A hypoglycemic thiazolidinedione had been proven to increase the activity of the complex IV, which is part of the mitochondrial respiratory chain. This has been shown to increase mitochondrial function thus reduces the further destruction mitochondrial dysfunction causes in diseases like PD. (Pienaar&Chinnery, 2012) The involvement of catecholamine inhibitors have also been shown to increase the availability of dopamine in the body thus decrease PD effects. Along with that, Estrogen and vitamin supplements have also been considered important for management. (Pienaar&Chinnery, 2012) Seeing how mitochondria are involved intensely in neurodegenerative disorders, mitochondrial targeted peptides have been considered of much importance. These proteins decrease the production of ROS by mitochondria thus decrease mitochondrial swelling and apoptosis in the long run. (Pienaar & Chinnery, 2012)

Exercise training has also shown that improvement in patients with single mtDNa deletions problems. When the muscle satellite cells get activated, it permits WT mTDNA to repopulate muscle and thus it decreases the mutant load to the mitochondria's. (Pitceathly et al., 2012)

Prevention of Mitochondrial medicine

Since most of the mitochondrial diseases are either due to mutated mitochondrial or nuclear DNA, the best approach is to fix the mutations before the babies are born. It is known that mitochondrial genes are transmitted only by the mother thus both the baby and mother can be checked for mutations beforehand. Even though one cannot readily predict that any certain gene will cause a mutation, mutated DNA can be manipulated and changing into wild-type mtDNa. (Yabuuchi et al., 2012) Approaches present to this are known as metaphase chromosome transfer, pronuclear transfer, ooplasmic transfer and germinal vesicle transfer.

Prenatal diagnosis serves as a crucial means of preventing the occurrence of mitochondrial mutations. This form however is hindered by factors such as coexistence of non-mutated and mutated mtDNA and maternal inheritance. Another issue arises is that even though a child can be cured and not have mitochondrial mutation. For instance, after fixing her DNA, she can have 3% of mutant DNA, and live a healthy life. Nonetheless, she can still transfer it to his or her child. (Yabuuchi et al., 2012) The major concept in all the methods mentioned earlier is that the mutated DNA is changed with the healthy DNA.

Discussion

There was a time when Parkinson's disease remained a mystery to all. After extensive research, several causative factors have been identified as the culprit behind it. Defective genes have been linked with other factors like age, environmental factors and tendencies of abnormal proteins to be made. A gene that codes for the protein alpha-synuclein is known to be responsible for the production of aggregates of their protein into the brain substance. Certain mutations and wrong genetic sequences make proteins sway away from their native folding pattern and thus cause their accumulation and lead to degenerative orders. Apart from protein misfolding and accumulation, abnormal mitochondrial DNA has also been blamed for the inheritance of PD. Three of the gene products responsible for causing PD are of mitochondrial origin. (Schapira, 2012) Other genes linked to PD and belonging to mitochondria are PARK and PINK1 which have been discussed in detail above. These genes have caused mitochondrial function to decline and worsen the progression of degenerative diseases like Parkinson's.

Conclusion

Degenerative diseases become apparent in a person due to the amalgamation of many factors. Abnormal proteins, increased oxidative stress and mutant DNA are some of the highlighted factors. All these causative agents are interlinked amongst each other and thus predispose a person to attaining a disorder. Since the neurons require a lot of energy, they rely heavily on adequate mitochondrial function. This reliance coupled with defective mitochondrial DNA sets the stage for a degenerative condition to ensue. Attempts are being made to target mitochondrial DNA so the prevalence of getting Parkinson's disease and many other age-linked disorder decreases.