Mitochondrial genetics
From EvoWiki
In genetics, Mitochondria are the powerhouses of the cell, producing ATP through the metabolism of pyruvic acid and other energy containing molecules. They also help detoxify the cell by catabolic processes in which they breakdown fatty and amino acids.
Why It Is Important
Because they provide 36 molecules of ATP per glucose molecule in contrast to the 2 ATP molecules produced by glycolysis, mitochondria are essential to all higher organisms for sustaining life. This is why slight problems with any one of the numerous enzymes used by the mitochondria can be devastating to the cell, and in turn, to the organism. Also, mitochondria specialize depending on what cells they exist in, and they perform specific functions at different stages in development of the cell based on the cell’s needs.
Having a greater understanding of the genetic mutations which affect mitochondria can not only give us a much better understanding of how our bodies and cells work, evolution, and give us insight into methods for successful therapeutic tissue and organ cloning, but it can also lead us to better treatments and possibly even cures for many of the diseases that devastate many individuals and families.
Mitochondrial Membrane Complexes
The processes carried out by the electron transport chain are mediated by protein complexes (named Complexes I-V, DHO-QO, ETF-QO, and ANT). Complex I, or NADH dehydrogenase:ubiquinone oxidoreductase, uses the energy in NADH and uses to pump protons into the intermembrane space of the mitochondrion, pumping 4 protons per electron and passing energy on to complex III (coenzyme Q or ubiquinone:Cytochrome bc1 oxidoreductase) in the form of an electron. Complex II (succinate:CoQ Oxidoreductase) accepts energy from FADH2 produced in the citric acid cycle and passes it to complex III. Complex III pumps 4 protons per electron and passes electrons to complex IV. Complex IV only pumps 2 protons into the space between the mitochondrion’s two membranes before passing the electron to O2 which reacts to form water. Complex V (ATP synthase:Proton Translocase) is a rotary complex which allows approximately (determining the actual number is very difficult) 10 protons to enter the mitochondrial matrix along their concentration gradients. It uses the energy from the gradient to form the bond between ADP and the phosphate group to create ATP. The electron transfer flavoprotein:CoQ Oxidoreductase complex is also an electron-transporting molecule and is involved in the breakdown of fatty acids and amino acids. ANT (adenine nucleotide translocator) is also involved in oxidative phosphorylation as an energy carrying molecule. Each of these eight complexes plays a vital role in the health of the cell and any slight mutation in any one of the proteins that make up these complexes can lead to cell death or stress, which can both in turn lead to a number of diseases.
Mitochondrial Genome
Mitochondria, like cells, and unlike most other organelles, have their own DNA (named mtDNA). The mtDNA is a circular molecule and in most animals codes for 13 or 14 proteins involved in the electron transport chain, 2 rRNA subunits, and 22 tRNA molecules. There are many more proteins involved in the electron transport chain than these 13 or 14. The rest come from the translation of nuclear DNA of the cell. Coding for mitochondrial proteins is done by around 3000 genes, of which only around 37 are found in mitochondrial DNA. Most of those 3000 genes are involved in a variety of processes other than ATP production. Only about 3% of them code for ATP production proteins. This means most of the genetic information coding for the protein makeup of mitochondria is in chromosomal DNA and is involved in processes other than ATP synthesis. This increases the chances that a mutation that will affect a mitochondrion will occur in chromosomal DNA, which is inherited in a Mendelian pattern, and that the mutation will affect a specific tissue due to its specific needs, whether those may be high energy requirements or a need for the catabolism or anabolism of a specific neurotransmitter or nucleic acid. Because several copies of the mitochondrial genome are carried by the each mitochondrion, mitochondrial mutations can be inherited maternally by mtDNA mutations which are present in mitochondria inside the oocyte before fertilization, or (as stated above) through mutations in the chromosomes.
The actual mitochondrial genome is a circular molecule with around 37 genes (the number varies greatly from species to species). In humans, the heavy strand carries 28 genes and the light strand carries only 9 genes. Eight of the 9 genes on the light strand code for mitochondrial tRNA molecules. Humans also have 16,569 nucleotide pairs in their mtDNA. The entire molecule is regulated by only one regulatory region which contains the origins of replication of both heavy and light strands. Normally, there are between 2 and 10 copies of the mtDNA molecule in each mitochondrion. The entire human mitochondrial DNA molecule has been mapped. (The Catalana Society of Neurology Societat Catalana de Neurologia provides an excellent diagram of the human mitochondrial genome at the bottom of this website. Another great picture of the molecule can be found thanks to the Mitochondrial Human Genome Report.) The rate of mutation in mtDNA is calculated to be about ten times greater than that of nuclear DNA. This high mutation rate causes all mitochondria to be very different, not only among different species but even within the same species. It is calculated that if two humans are chosen randomly and their mtDNA is tested, they will have an average of between fifty and seventy different nucleotides. This may not seem like much, but when compared to the total number of nucleotides of a human mitochondrial DNA molecule (16,569), as much as .42% of the mtDNA varies between two people.
Detailed Inheritance Patterns of Mitochondrial Diseases
Because mitochondrial diseases can be inherited both maternally and through chromosomal inheritance, the way in which they are passed on from generation to generation can vary greatly depending on the disease. Mitochondrial genetic mutations that occur in the nuclear DNA can occur in any of the chromosomes (depending on the species). Mutations inherited through the chromosomes can be autosomal dominant or recessive and can also be sex-linked dominant or recessive. Chromosomal inheritance follows normal Mendelian laws, despite the fact that the phenotype of the disease may be masked. Because of the complex ways in which mitochondrial and nuclear DNA “communicate” and interact, even seemingly simple inheritance is hard to diagnose. A mutation in chromosomal DNA may change a protein that regulates (up or down regulates) the production of another certain protein in the mitochondria or the cytoplasm and may lead to slight, if any, noticeable symptoms. On the other hand, there are some devastating mtDNA mutations that are easy to diagnose because of their widespread damage to muscular, neural, and/or hepatic (among other high energy and metabolism dependant) tissues and due to the fact that they are present in the mother and all the offspring. Mitochondrial genome mutations are passed on 100% of the time from mother to all her offspring. Because the mitochondria within the fertilized oocyte is what the new life will have to begin with (in terms of mtDNA), and because the number of affected mitochondria varies from cell (in this case, the fertilized oocyte) to cell depending both on the number it inherited from its mother cell and environmental factors which may favor mutant or wildtype mitochondrial DNA, and because the number of mtDNA molecules in the mitochondria varies from around two to ten, the number of affected mtDNA molecules inherited to a specific offspring can vary greatly. It is possible, even in twin births, for one baby to receive more than half mutant mtDNA molecules while the other twin may receive only a tiny fraction of mutant mtDNA molecules with respect to wildtype (depending on how the twins divide from each other and how many mutant mitochondria happen to be on each side of the division). In a few cases, some mitochondria or a mitochondrion from the sperm cell enters the oocyte but paternal mitochondria are actively decomposed.
The Genetic Code
The genetic code is, for the most part, universal. There are few exceptions to this statement. Mitochondrial genetics includes a some of these exceptions. For most organisms the stop codons are “UAA”, “UAG”, and “UGA”. The stop codons for vertebrate mitochondria are “AGA” and “AGG”. “AUA” codes for Isoleucine in most organisms but it codes for Methionine in vertebrate mitochondrial mRNA/tRNA and “UGA” which is normally associated as a stop codon codes for Threonine. There are many other variations among the codes used by other mitochondrial m/tRNA which gives us good examples of mutations that happened to not be harmful to the organisms they occurred in. Furthermore, they can be used as a tool (along with other mutations among the mtDNA/RNA of different species) to determine relative proximity of common ancestry of related species. Using these techniques, it is estimated that the first mitochondria (or more correctly, aerobic prokaryote inside an anaerobic eukaryote in a symbiotic relationship) evolved, or was consumed, or developed around 1.5 billion years ago.
Mitochondrial Replication, Repair, Transcription, and Translation
Mitochondrial replication is controlled by chromosomes in the nucleus and is specifically suited to make as many mitochondria as that particular cell needs at the time. Mitochondrial polymerase is used in the copying of mtDNA during replication. Because the two (heavy and light) strands on the circular mtDNA molecule have different origins of replication, it replicates in a D-loop (displacement) configuration. One strand begins to replicate first, displacing the other strand. This continues until replication reaches the origin of replication on the other strand, at which point the other strand beings replicating in the opposite direction. This results in two new mtDNA molecules. Each mitochondria has several copies of the mtDNA molecule and the number of mtDNA molecules is a limiting factor in mitochondrial fission. After the mitochondrion has enough mtDNA, membrane area, and membrane proteins, it can undergo fission (very similar to that which bacteria use) to become two mitochondria. Evidence suggests that mitochondria can also undergo fusion and exchange (in a form of crossover) genetic material among each other. Mitochondria sometimes form large matrices in which fusion, fission, and protein exchanges are constantly occurring. mtDNA shared among mitochondria (despite the fact that they can undergo fusion).
Mitochondrial DNA is prone to damage from free oxygen radicals from mistakes that occur during the production of ATP through the electron transport chain. These mistakes can be caused by genetic disorders, cancer, and temperature variations. These radicals can damage mtDNA molecules or change them, making it hard for mitochondrial polymerase to replicate them. Both cases can lead to deletions, rearrangements, and other mutations. Recent evidence has suggested that mitochondria have enzymes that proofread mtDNA and fix mutations that may occur due to free radicals. It is believed that a DNA recombinase found in mammalian cells is also involved in a repairing recombination process. Deletions and mutations due to free radicals have been associated with the aging process. It is believed that radicals cause mutations which lead to mutant proteins, which in turn lead to more radicals. This process takes many years and is associated with some aging processes involved in oxygen-dependent tissues such as brain, heart, muscle, and kidney. Auto-enhancing processes such as these are possible causes of degenerative diseases including Parkinson’s, Alzheimer’s, and coronary artery disease.
Mitochondrial transcription and translation are controlled by the nucleus. Human mitochondria have three promoters, H1, H2, and L (heavy strand 1, heavy strand 2, and light strand promoters). The H1 promoter transcribes the entire heavy strand and the L promoter transcribes the entire light strand. The H2 strand causes the transcription of the two mitochondrial rRNA molecules. When transcription takes place on the heavy strand a polycistronic transcript is created. The light strand produces either small transcripts, which can be used as primers, or one long transcript. The transcripts are then cut into functional tRNA, rRNA, and mRNA molecules. Mitochondrial translation is still not very well understood. In vitro translations have still not been successful, probably due to the difficulty of isolating sufficient mt mRNA, functional mt rRNA, and possibly the complicated changes which the mRNA undergoes before it is translated.
Chromosomally Mediated mtDNA Replication Errors
Because mitochondrial growth and fission are mediated by the nuclear DNA, mutations in nuclear DNA can have a wide array of effects on mtDNA replication. Despite the fact that the loci for some of these mutations have been found on human chromosomes, specific genes and proteins involved have not yet been isolated. Mitochondria need a certain protein to undergo fission. If this protein (made by the nucleus) is not present, the mitochondria grow but they do not divide. This leads to giant, inefficient mitochondria. Mistakes in chromosomal genes or their products can also affect mitochondrial replication more directly by inhibiting mitochondrial polymerase and can even cause mutations in the mtDNA directly and indirectly. Indirect mutations are most often caused by radicals created by defective proteins made from nuclear DNA.
Mitochondrial Diseases
Mitochondrial diseases range in severity from almost not diagnosable to fatal. They also range in cause from inherited to acquired mutations (although acquired mutations that cause disease are very rare). A certain mutation can cause several different diseases depending on the severity of the problem in the mitochondria and the tissue the affected mitochondria are in. Conversely, several different mutations may present themselves as the same disease. This almost patient-specific characterization of mitochondrial diseases makes them very hard to accurately diagnose and trace. Some diseases are observable at or even before birth (most causing death) while others do not show themselves until late adulthood. This is because the number of mutant versus wildtype mitochondria varies from cell to cell and tissue to tissue, and is always changing. Because cells have multiple mitochondria, different mitochondria in the same cell can have different variations of the mtDNA genome. This condition is referred to as heteroplasmy. When a certain tissue reaches a certain ration of mutant versus wildtype mitochondria, a disease will present itself. The ration varies from person to person and tissue to tissue (depending on its specific energy, oxygen, and metabolism requirements, and the effects of the specific mutation). Mitochondrial diseases are very numerous and different. They include diabetes, cancer, heart disease, lactic acidosis, lethal infantile myocardiopathy, Myopathy, osteoporosis, Alzheimer's disease and Parkinsons's disease, stroke, and many more. mtDNA mutations are even believed to be involved in the aging process.
External Links
Sources
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