19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations in Chapter 19 Oxidative Phosphorylation

19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations

Mitochondria contain their own genome, a circular, double-stranded DNA (mtDNA) molecule. Each of the hundreds or thousands of mitochondria in a typical cell has about five copies of this genome. The human mitochondrial chromosome (Fig. 19-40) contains 37 genes (16,569 bp), including 13 that encode subunits of proteins of the respiratory chain (Table 19-6); the remaining genes code for rRNA and tRNA molecules essential to the protein-synthesizing machinery of mitochondria. To synthesize these 13 protein subunits, mitochondria have their own ribosomes, distinctly different from those in the cytoplasm. The great majority of mitochondrial proteins — about 1,200 different types — are encoded by nuclear genes, synthesized on cytoplasmic ribosomes, then imported into and assembled in the mitochondria (Chapter 27).

A figure shows a map of human mitochondrial D N A showing genes and mutations. — FIGURE 19-40 Mitochondrial genes and mutations. A map of human mitochondrial DNA, showing the genes that encode proteins of Complex I, the NADH dehydrogenase (*ND1* to *ND6*); the cytochrome b of Complex III (*Cyt b*); the subunits of cytochrome oxidase, Complex IV (*COI* to *COIII*); and two subunits of ATP synthase (*ATPase6* and *ATPase8*). The colors of the genes correspond to those of the complexes shown in Figure 19-7. Also included here are the genes for ribosomal RNAs (*rRNA*) and for some mitochondrion-specific transfer RNAs; tRNA specificity is indicated by the one-letter codes for amino acids. Arrows indicate the positions of mutations that cause Leber hereditary optic neuropathy (LHON) and myoclonic epilepsy with ragged-red fibers (MERRF) syndrome. Numbers in parentheses indicate the position of the altered nucleotides (nucleotide 1 is at the top of the circle, and numbering proceeds counterclockwise). [Information from M. A. Morris, *J. Clin. Neuroophthalmol.* 10:159, 1990.]

A key shows that pink equals complex Roman numeral 1, blue equals complex Roman numeral 3, green equals complex Roman numeral 4, orange equals A T P synthase, brown equals transfer R N A, beige equals ribosomal R N A, and gray equals control region of D N A. The chromosome is circular. Gene names are italicized. A gray bar spans the twelve o’clock position from a brown bar labeled F to the left to a brown bar labeled P to the right adjacent to another brown bar labeled T. An arrow pointing to the middle of the gray bar at the twelve o’clock position reads, 0/16,569. A blue bar labeled C y t b is next and extends to the one o’clock position with an arrow pointing to the middle labeled, L H O N (15,257). There is a brown bar labeled E, then a short pink piece labeled N D 6 that extends to the two o’clock position followed by a long pink bar labeled N D 5 that extends past the three o’clock position. Next, there are three brown bars: L, S, and then H. A pink bar labeled N D 4 extends past the four o’clock position and an arrow labeled L H O N (11,778) points to its center. It is followed by a small band labeled N D 4 L that ends at the five o’clock position at a brown bar labeled R, followed by a pink piece labeled N D 3, followed by a brown bar labeled G, followed by a longer green piece labeled C O Roman numeral 3, followed by a longer orange piece labeled A T P ase 6 that meets a light blue bar and then an orange piece labeled A T P ase 8 that ends at the six o’clock position. A brown bar labeled K and indicated by an arrow labeled M E R R F (8,344) is next, followed by a green piece labeled C O Roman numeral 2 and two brown bars labeled D and then S. A long green piece labeled C O Roman numeral 1 begins just before the seven o’clock position and continues to the eight o’clock position. Next, there are brown bars Y, then C, then a thin gray bar, then brown bar N, brown bar A, and brown bar W. A pink piece labeled N D 2 runs almost to the nine o’clock position, then there are brown bars M, Q, and I. A pink piece labeled N D 1 begins just above the nine o’clock position and has an arrow labeled L H O N (4,160) pointing to its lower half and an arrow labeled L H O N (3,460) pointing to its upper half. There is a brown bar labeled L at the ten o’clock position, then a long beige piece labeled 16 S R N A that extends to the eleven o’clock position. Next, there is a brown bar labeled V, then a beige piece labeled 12 S r R N A, then a brown bar labeled F to the left of the gray bar that runs across the twelve o’clock position. All data are approximate.

TABLE 19-6 Respiratory Proteins Encoded by Mitochondrial Genes in Humans
Complex	Number of subunits	Number of subunits encoded by mtDNA
I NADH dehydrogenase	45	7
II Succinate dehydrogenase	4	0
III Ubiquinone:cytochrome c oxidoreductase	11	1
IV Cytochrome oxidase	13	3
V ATP synthase	8	2

Mitochondria Evolved from Endosymbiotic Bacteria

The existence of mitochondrial DNA, ribosomes, and tRNAs supports the theory of the endosymbiotic origin of mitochondria (see Fig. 1-37), which holds that the first organisms capable of aerobic metabolism, including respiration-linked ATP production, were bacteria. Primitive eukaryotes that lived anaerobically (by fermentation) acquired the ability to carry out oxidative phosphorylation when they established a symbiotic relationship with bacteria living in their cytosol. After a long period of evolution and the movement of many bacterial genes into the nucleus of the “host” eukaryote, the endosymbiotic bacteria eventually became mitochondria.

This hypothesis presumes that early free-living bacteria had the enzymatic machinery for oxidative phosphorylation. And it predicts that their modern bacterial descendants must have respiratory chains closely similar to those of modern eukaryotes. They do. Aerobic bacteria carry out NAD-linked electron transfer from substrates to $O_{2}$ $upper O Subscript 2$ , coupled to the phosphorylation of cytosolic ADP. The dehydrogenases are located in the bacterial cytosol, and the respiratory chain in the plasma membrane. The electron carriers translocate protons outward across the plasma membrane as electrons are transferred to $O_{2}$ $upper O Subscript 2$ . Bacteria such as E. coli have $F_{o} F_{1}$ $upper F Subscript o Baseline upper F Subscript 1$ complexes in their plasma membranes; the $F_{1}$ $upper F Subscript 1$ portion protrudes into the cytosol and catalyzes ATP synthesis from ADP and $P_{i}$ $upper P Subscript i$ as protons flow back into the cell through the proton channel of $F_{o}$ $upper F Subscript o$ .

The respiration-linked extrusion of protons across the bacterial plasma membrane also provides the driving force for other processes. Certain bacterial transport systems bring about uptake of extracellular nutrients (lactose, for example) against a concentration gradient, in symport with protons. And the rotary motion of bacterial flagella is provided by “proton turbines,” molecular rotary motors driven not by ATP but directly by the transmembrane electrochemical potential generated by respiration-linked proton pumping (Fig. 19-41). It seems likely that the chemiosmotic mechanism evolved early, before the emergence of eukaryotes.

A figure shows the rotation of bacterial flagella by proton-motive force. — FIGURE 19-41 Rotation of bacterial flagella by proton-motive force. The shaft and rings at the base of the flagellum make up a rotary motor that has been called a “proton turbine.” Protons ejected by electron transfer flow back into the cell through the turbine, causing rotation of the shaft of the flagellum. This motion differs fundamentally from the motion of muscle and of eukaryotic flagella and cilia, for which ATP hydrolysis is the energy source.

A curved end of a bacterium is shown. It has an outer membrane, a blue region labeled peptidoglycan and periplasmic space, and then an inner (plasma) membrane. A small purple bar labeled respiratory chain is shown just to the left of a series of discs that extend across both membranes and the periplasmic space. A thick cylinder extends from the top disc with a clockwise arrow pointing around it and a thin wavy structure labeled flagellum extends out from this cylinder. A clockwise black arrow is shown around a narrow region between two discs and text below reads rotary motor. Red highlighted H plus beneath the membrane has a red arrow through the respiratory chain and out through the periplasmic space and outer membrane to red highlighted H plus, from which an arrow points through the stack of discs and back out to H plus below ready to continue the cycle.

Mutations in Mitochondrial DNA Accumulate throughout the Life of the Organism

The respiratory chain is the major producer of reactive oxygen species in cells, so mitochondrial contents, including the mitochondrial genome, suffer the greatest exposure to, and damage by, ROS. Moreover, the mitochondrial DNA replication system is less effective than the nuclear system at correcting mistakes made during replication and at repairing DNA damage. As a consequence, defects in mtDNA accumulate over time. One theory of aging is that this gradual accumulation of defects is the primary cause of many of the “symptoms” of aging, which include, for example, progressive weakening of skeletal and heart muscle.

A unique feature of mitochondrial inheritance is the variation among individual cells, and between one individual organism and another, in the effects of a mtDNA mutation. A typical cell has hundreds or thousands of mitochondria, each with multiple copies of its own genome (Fig. 19-2b). Animals inherit essentially all of their mitochondria from the female parent. Eggs are large and contain $10^{5}$ $10 Superscript 5$ or $10^{6}$ $10 Superscript 6$ mitochondria; sperm are much smaller and contain far fewer mitochondria — perhaps 100 to 1,000. Furthermore, there is an active mechanism for targeting sperm-derived mitochondria for degradation in the fertilized egg. Just after fertilization, maternal phagosomes migrate to the site of sperm entry, engulf sperm mitochondria, and degrade them.

Suppose that, in a female organism, damage to one mitochondrial genome occurs in a germ cell from which oocytes develop, such that the germ cell contains mainly mitochondria with wild-type genes but one mitochondrion with a mutant gene. During the course of oocyte maturation, as this germ cell and its descendants repeatedly divide, the defective mitochondrion replicates and its progeny, all defective, are randomly distributed to daughter cells. Eventually, the mature egg cells contain different proportions of the defective mitochondria. When an egg cell is fertilized and undergoes the many divisions of embryonic development, the resulting somatic cells differ in their proportion of mutant mitochondria (Fig. 19-42a). This heteroplasmy (in contrast to homoplasmy, in which every mitochondrial genome in every cell is the same) results in mutant phenotypes of varying degrees of severity. Cells (and tissues) containing mostly wild-type mitochondria have the wild-type phenotype; they are essentially normal. Other heteroplasmic cells have intermediate phenotypes, some almost normal, others (with a high proportion of mutant mitochondria) abnormal (Fig. 19-42b). If the abnormal phenotype is associated with a disease, individuals with the same mtDNA mutation may have disease symptoms of differing severity — depending on the number and distribution of affected mitochondria.

A two-part figure shows how heteroplasmy occurs in an illustration in part a and then shows different phenotypes resulting from heteroplasmy in part b. — FIGURE 19-42 Heteroplasmy in mitochondrial genomes. (a) When a mature egg cell is fertilized, all of the mitochondria in the resulting diploid cell (zygote) are maternal; none come from the sperm. If some fraction of the maternal mitochondria have a mutant gene, the random distribution of mitochondria during subsequent cell divisions yields some daughter cells with mostly mutant mitochondria, some with mostly wild-type mitochondria, and some in between. Thus daughter cells show a varying degree of heteroplasmy. (b) Different degrees of heteroplasmy produce different cellular phenotypes. This section of human muscle tissue is from an individual with defective cytochrome oxidase. The cells were stained so that wild-type cells are blue and cells with mutant cytochrome oxidase are brown. As the micrograph shows, different cells in the same tissue are affected to different degrees by the mitochondrial mutation. [(b) Courtesy of Rob Taylor. Reprinted with permission from R. W. Taylor and D. M. Turnbull, *Nat. Rev. Genet.* 6:389, 2005, Fig. 2a.]

Part a shows a yellow circle labeled parent cell that contains a gray oval nucleus in the center, three orange mutant mitochondria, and six gray wild-type mitochondria. An arrow labeled contents double points right to a larger cell with two of each mitochondrion, shown in pairs. Two arrows point down to show cell division. This produces two daughter cells. The left-hand daughter cell has five orange mitochondria and four gray mitochondria. The right-hand daughter cell has one orange mitochondrion and eight gray mitochondria. Two arrows point down from each daughter cell accompanied by text reading, cells double and divide. The left-hand daughter cell produces a largely mutant cell with seven orange mitochondria and two gray mitochondria to the left of a cell with three orange mitochondria and six gray mitochondria. The right-hand daughter cell produces a largely wild type cell with two orange mitochondria and seven gray mitochondria and a fully wild type cell with nine gray mitochondria. A double-headed arrow beneath the three cells on the left, ranging from largely mutant to largely wild type, is labeled heteroplasmy and gradually changes from orange on the left to gray on the right. A gray bar labeled homoplasmy is shown beneath the fully wild type cell on the right. Part b shows a micrograph of many cells that range in color from brown to light brown to light blue to dark blue.

Some Mutations in Mitochondrial Genomes Cause Disease

About 1 in 5,000 people have a disease-causing mutation in a mitochondrial protein that reduces the cell’s capacity to produce ATP. A growing number of these diseases have been attributed to mutations in mitochondrial genes. Some tissues and cell types — neurons, myocytes of both skeletal and cardiac muscle, and β cells of the pancreas — are less able than others to tolerate lowered ATP production and are therefore more affected by mutations in mitochondrial proteins.

A group of genetic diseases known as the mitochondrial encephalomyopathies affect primarily the brain and skeletal muscle. These diseases are invariably inherited from the mother, because, as noted above, a developing embryo derives all its mitochondria from the egg. The rare disease Leber hereditary optic neuropathy (LHON) affects the central nervous system, including the optic nerves, causing bilateral loss of vision in early adulthood. A single base change in the mitochondrial gene ND4 (Fig. 19-40) changes an Arg residue to a His residue in a polypeptide of Complex I, and the result is mitochondria partially defective in electron transfer from NADH to ubiquinone. Although these mitochondria can produce some ATP by electron transfer from succinate, they apparently cannot supply sufficient ATP to support the very active metabolism of neurons, including the optic nerve. A single base change in the mitochondrial gene for cytochrome b, a component of Complex III, also produces LHON, demonstrating that the pathology results from a general reduction of mitochondrial function, not specifically from a defect in electron transfer through Complex I.

A mutation in the mitochondrial gene ATP6 affects the proton pore in ATP synthase, leading to low rates of ATP synthesis while leaving the respiratory chain intact. Oxidative stress due to the continued supply of electrons from NADH increases the production of ROS, and the damage to mitochondria caused by ROS sets up a vicious cycle. Half of individuals with this mutant gene die within days or months of birth.

Myoclonic epilepsy with ragged-red fibers (MERRF) syndrome is caused by a mutation in the mitochondrial gene that encodes a tRNA specific for lysine $({tRNA}^{Lys})$ $left-parenthesis tRNA Superscript Lys Baseline right-parenthesis$ . This disease, characterized by uncontrollable muscular jerking, results from defective production of several of the proteins that require mitochondrial tRNAs for their synthesis. Skeletal muscle fibers of individuals with MERRF syndrome have abnormally shaped mitochondria that sometimes contain paracrystalline structures (Fig. 19-43). Other mutations in mitochondrial genes are believed to be responsible for the progressive muscular weakness that characterizes mitochondrial myopathy and for enlargement and deterioration of the heart muscle in hypertrophic cardiomyopathy.

A micrograph shows a round structure that is mostly gray inside except for a rectangular structure consisting of many parallel dark lines that extend down slightly on the right end. — FIGURE 19-43 Paracrystalline inclusions in MERRF syndrome mitochondrion. Electron micrograph of an abnormal mitochondrion from the muscle of an individual with MERRF syndrome, showing the paracrystalline protein inclusions sometimes present in the mutant mitochondria. [From Regionalized Pathology Correlates with Augmentation of mtDNA Copy Numbers in a Patient with Myoclonic Epilepsy with Ragged-Red Fibers (MERRF-Syndrome). *PLOS ONE,* Anja Brinckmann et al., October 20, 2010. https://doi.org/10.1371/journal.pone.0013513]

If a prospective mother is known to carry a pathogenic mitochondrial gene, the technique of mitochondrial donation can circumvent the passage of that mutant gene to her offspring. A prospective mother’s nuclear genes are microscopically transplanted into an enucleated ovum from a donor with healthy mitochondria, then the ovum is fertilized in vitro and the resulting embryo is transplanted into the mother’s uterus. This and similar “three-parent baby” procedures, which were approved in the United Kingdom in 2015, raise ethical issues that are being vigorously debated.

Mitochondrial disease can also result from mutations in any of the ~1,200 nuclear genes that encode mitochondrial proteins. For example, a mutation in one of the nuclear-encoded proteins of Complex IV, COX6B1, results in severe defects in brain development and thickened walls of the heart muscle. Other nuclear genes encode proteins essential for the assembly of mitochondrial complexes. Mutations in these genes can also lead to serious mitochondrial disease.

A Rare Form of Diabetes Results from Defects in the Mitochondria of Pancreatic β Cells

The insulin so important to glucose homeostasis in all humans is produced and exported from pancreatic β cells. Insulin export hinges on the ATP concentration in those cells. When blood glucose is high, β cells take up glucose and oxidize it by glycolysis and the citric acid cycle, raising [ATP] above a threshold level (Fig. 19-44). When [ATP] exceeds this threshold, an ATP-gated $K^{+}$ $upper K Superscript plus$ channel in the plasma membrane closes, depolarizing the membrane and triggering insulin release (see Fig. 23-24).

A figure shows how a mitochondrial defect can prevent insulin secretion. — FIGURE 19-44 A mitochondrial defect prevents insulin secretion. In the normal situation, as depicted here, when the blood glucose level rises, production of ATP in β cells increases. ATP, by blocking $K^{+}$ $upper K Superscript plus$ channels, depolarizes the plasma membrane and thus opens voltage-gated ${Ca}^{2 +}$ $Ca Superscript 2 plus$ channels. The resulting influx of ${Ca}^{2 +}$ $Ca Superscript 2 plus$ triggers exocytosis of insulin-containing secretory vesicles, releasing insulin. When oxidative phosphorylation in β cells is defective, [ATP] is never sufficient to trigger this process, and insulin is not released.

FIGURE 19-44 A mitochondrial defect prevents insulin secretion. In the normal situation, as depicted here, when the blood glucose level rises, production of ATP in β cells increases. ATP, by blocking $K^{+}$ $upper K Superscript plus$ channels, depolarizes the plasma membrane and thus opens voltage-gated ${Ca}^{2 +}$ $Ca Superscript 2 plus$ channels. The resulting influx of ${Ca}^{2 +}$ $Ca Superscript 2 plus$ triggers exocytosis of insulin-containing secretory vesicles, releasing insulin. When oxidative phosphorylation in β cells is defective, [ATP] is never sufficient to trigger this process, and insulin is not released.

Light blue horizontal bars above and below a cell are labeled blood. A yellow pancreatic beta cell is shown between these two blood vessels. A vertical channel labeled glucose transporter is shown at the upper right. Glucose in the blood is shown with an arrow pointing down through the channel to the inside of the cell. An arrow points down from glucose to pyruvate at the upper left corner of a gray illustration of a mitochondrion. An arrow points down from pyruvate and branches to a vertical arrow to C O 2 below the mitochondrion and to an arrow labeled respiration that curves to run the length of the mitochondrion to A T P to the upper right. A dashed arrow points from A T P to a red circle containing a red “X” next to a horizontal A T P-gated K plus channel. K plus is shown inside of the cell with an arrow pointing through the channel to K plus outside of the cell. A horizontal voltage-gated C a 2 plus channel is shown below. C a 2 plus outside of the cell has an arrow pointing through the channel to C a 2 plus inside of the cell. A gray box between these two channels reads, A T P closes K plus channel; resulting depolarization opens C a 2 plus channel. An arrow points from C a 2 plus inside of the cell through seven orange circles labeled insulin granules to a green circle containing a green triangle against the membrane at the bottom right of the cell. An invagination in the membrane contains many red dots that expand out into the blood below. Accompanying text reads, insulin secretion.

Normal insulin release can be compromised in several ways. Pancreatic β cells with defects in any aspect of oxidative phosphorylation may not be able to increase [ATP] above this threshold, and the resulting failure of insulin release effectively produces diabetes. For example, defects in the gene for glucokinase, the hexokinase IV isozyme present in β cells, lead to a rare form of diabetes called MODY2 (maturity onset diabetes of the young); low glucokinase activity prevents the generation of ATP concentrations above the threshold needed to trigger insulin secretion. Mutations in the mitochondrial ${tRNA}^{Lys}$ $tRNA Superscript Lys$ or ${tRNA}^{Leu}$ $tRNA Superscript Leu$ genes also compromise mitochondrial ATP production by limiting the expression of electron transfer components encoded in the mitochondrial DNA. Type 2 diabetes mellitus is common among individuals with these defects (although such cases make up a very small fraction of all cases of diabetes).

When nicotinamide nucleotide transhydrogenase, which is part of the mitochondrial defense against ROS (Fig. 19-18), is genetically defective, the accumulation of ROS damages mitochondria, slowing ATP production and blocking insulin release by β cells (Fig. 19-44). Damage caused by ROS, including damage to mtDNA, may also underlie other human diseases; there is some evidence for its involvement in Alzheimer, Parkinson, and Huntington diseases and in heart failure, as well as in aging.

SUMMARY 19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations

A small proportion of human mitochondrial proteins, 13 in all, are encoded by the mitochondrial genome and synthesized in mitochondria. About 1,200 mitochondrial proteins are encoded by nuclear genes and imported into mitochondria after their synthesis.
Mitochondria arose from aerobic bacteria that entered into an endosymbiotic relationship with ancestral eukaryotes.
Mutations in the mitochondrial genome accumulate over the life of the organism. Mutations in nuclear or mitochondrial genes that encode components of the respiratory chain, ATP synthase, and the ROS-scavenging system, and even in tRNA genes, can cause a variety of human diseases, which often most severely affect muscle, heart, pancreatic β cells, and brain.
It is possible to combine the mitochondria from one woman with the nuclear genes of another to create an ovum free of a mutation that would have led to a mitochondrial disease.
Mitochondrial defects in pancreatic β cells that limit ATP production when glucose levels are high can compromise normal insulin release and give rise to a form of type 2 diabetes.