So far, we have considered how nuclear genes assort independently by virtue of their loci on different chromosomes. However, although the nucleus contains most of a eukaryotic organism’s genes, a distinct and specialized subset of the genome is found in the mitochondria, and, in plants, also in the chloroplasts. These subsets are inherited independently of the nuclear genome, and so they constitute a special case of independent inheritance, sometimes called extranuclear inheritance.

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Mitochondria and chloroplasts are specialized organelles located in the cytoplasm. They contain small circular chromosomes that carry a defined subset of the total cell genome. Mitochondrial genes are concerned with the mitochondrion’s task of energy production, whereas chloroplast genes are needed for the chloroplast to carry out its function of photosynthesis. However, neither organelle is functionally autonomous because each relies to a large extent on nuclear genes for its function. Why some of the necessary genes are in the organelles themselves and others are in the nucleus is still something of a mystery, which will not be addressed here.

Another peculiarity of organelle genes is the large number of copies present in a cell. Each organelle is present in many copies per cell, and, furthermore, each organelle contains many copies of its chromosome. Hence, each cell can contain hundreds or thousands of organelle chromosomes. Consider chloroplasts, for example. Any green cell of a plant has many chloroplasts, and each chloroplast contains many identical circular DNA molecules, the so-called chloroplast chromosomes. Hence, the number of chloroplast chromosomes per cell can be in the thousands, and the number can even vary somewhat from cell to cell. The DNA is sometimes seen to be packaged into suborganellar structures called nucleoids, which become visible if stained with a DNA-binding dye (Figure 3-18). The DNA is folded within the nucleoid but does not have the type of histone-associated coiling shown by nuclear chromosomes. The same arrangement is true for the DNA in mitochondria. For the time being, we will assume that all copies of an organelle chromosome within a cell are identical, but we will have to relax this assumption later.

Many organelle chromosomes have now been sequenced. Examples of relative gene size and spacing in mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) are shown in Figure 3-19. Organelle genes are very closely spaced, and, in some organisms, organelle genes can contain untranslated segments called introns. Note how most genes concern the chemical reactions taking place within the organelle itself: photosynthesis in chloroplasts and oxidative phosphorylation in mitochondria.

Organelle genes show their own special mode of inheritance called uniparental inheritance: progeny inherit organelle genes exclusively from one parent but not the other. In most cases, that parent is the mother, a pattern called maternal inheritance. Why only the mother? The answer lies in the fact that the organelle chromosomes are located in the cytoplasm and the male and female gametes do not contribute cytoplasm equally to the zygote. In regard to nuclear genes, both parents contribute equally to the zygote. However, the egg contributes the bulk of the cytoplasm, whereas the sperm contributes essentially none. Therefore, because organelles reside in the cytoplasm, the female parent contributes the organelles along with the cytoplasm, and essentially none of the organelle DNA in the zygote is from the male parent.

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Some phenotypic variants are caused by a mutant allele of an organelle gene, and we can use these mutants to track patterns of organelle inheritance. We will temporarily assume that the mutant allele is present in all copies of the organelle chromosome, a situation that is indeed often found. In a cross, the variant phenotype will be transmitted to progeny if the variant used is the female parent, but not if it is the male parent. Hence, generally, cytoplasmic inheritance shows the following pattern:

Indeed, this inheritance pattern is diagnostic of organelle inheritance in cases in which the genomic location of a mutant allele is not known.

Maternal inheritance can be clearly demonstrated in certain mutants of fungi. For example, in the fungus Neurospora, a mutant called poky has a slow-growth phenotype. Neurospora can be crossed in such a way that one parent acts as the maternal parent, contributing the cytoplasm (see Figure 3-9). The results of the following reciprocal crosses suggest that the mutant gene resides in the mitochondria (fungi have no chloroplasts):

Sequencing has shown that the poky phenotype is caused by a mutation of a ribosomal RNA gene in mtDNA. Its inheritance is shown diagrammatically in Figure 3-20. The cross includes an allelic difference (ad and ad+) in a nuclear gene in addition to poky; notice how the Mendelian inheritance of the nuclear gene is independent of the maternal inheritance of the poky phenotype.

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In some cases, cells contain mixtures of mutant and normal organelles. These cells are called cytohets, or heteroplasmons. In these mixtures, a type of cytoplasmic segregation can be detected, in which the two types apportion themselves into different daughter cells. The process most likely stems from chance partitioning of the multiple organelles in the course of cell division. Plants provide a good example. Many cases of white leaves are caused by mutations in chloroplast genes that control the production and deposition of the green pigment chlorophyll. Because chlorophyll is necessary for a plant to live, this type of mutation is lethal, and white-leaved plants cannot be obtained for experimental crosses. However, some plants are variegated, bearing both green and white patches, and these plants are viable. Thus, variegated plants provide a way of demonstrating cytoplasmic segregation.

The four-o’clock plant in Figure 3-21 shows a commonly observed variegated leaf and branch phenotype that demonstrates the inheritance of a mutant allele of a chloroplast gene. The mutant allele causes chloroplasts to be white; in turn, the color of the chloroplasts determines the color of cells and hence the color of the branches composed of those cells. Variegated branches are mosaics of all-green and all-white cells. Flowers can develop on green, white, or variegated branches, and the chloroplast genes of a flower’s cells are those of the branch on which it grows. Hence, in a cross (Figure 3-22), the maternal gamete within the flower (the egg cell) determines the color of the leaves and branches of the progeny plant. For example, if an egg cell is from a flower on a green branch, all the progeny will be green, regardless of the origin of the pollen. A white branch will have white chloroplasts, and the resulting progeny plants will be white. (Because of lethality, white descendants would not live beyond the seedling stage.)

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The variegated zygotes (bottom of Figure 3-22) demonstrate cytoplasmic segregation. These variegated progeny come from eggs that are cytohets. Interestingly, when such a zygote divides, the white and green chloroplasts often segregate; that is, they sort themselves into separate cells, yielding the distinct green and white sectors that cause the variegation in the branches. Here, then, is a direct demonstration of cytoplasmic segregation.

Given that a cell is a population of organelle molecules, how is it ever possible to obtain a “pure” mutant cell, containing only mutant chromosomes? Most likely, pure mutants are created in asexual cells as follows. The variants arise by mutation of a single gene in a single chromosome. Then, in some cases, the mutation-bearing chromosome may by chance increase in frequency in the population within the cell. This process is called random genetic drift. A cell that is a cytohet may have, say, 60 percent A chromosomes and 40 percent a chromosomes. When this cell divides, sometimes all the A chromosomes go into one daughter, and all the a chromosomes into the other (again, by chance). More often, this partitioning requires several subsequent generations of cell division to be complete (Figure 3-23). Hence, as a result of these chance events, both alleles are expressed in different daughter cells, and this separation will continue through the descendants of these cells. Note that cytoplasmic segregation is not a mitotic process; it does take place in dividing asexual cells, but it is unrelated to mitosis. In chloroplasts, cytoplasmic segregation is a common mechanism for producing variegated (green-and-white) plants, as already mentioned. In fungal mutants such as the poky mutant of Neurospora, the original mutation in one mtDNA molecule must have accumulated and undergone cytoplasmic segregation to produce the strain expressing the poky symptoms.

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In certain special systems such as in fungi and algae, cytohets that are “dihybrid” have been obtained (say, AB in one organelle chromosome and ab in another). In such cases, rare crossover-like processes can occur, but such an occurrence must be considered a minor genetic phenomenon.

Are there cytoplasmic mutations in humans? Some human pedigrees show the transmission of rare disorders only through females and never through males. This pattern strongly suggests cytoplasmic inheritance and points to a mutation in mtDNA as the reason for the phenotype. The disease MERRF (myoclonic epilepsy and ragged red fiber) is such a phenotype, resulting from a single base change in mtDNA. It is a disease that affects muscles, but the symptoms also include eye and hearing disorders. Another example is Kearns-Sayre syndrome, a constellation of symptoms affecting the eyes, heart, muscles, and brain that is caused by the loss of part of the mtDNA. In some of these cases, the cells of a sufferer contain mixtures of normal and mutant chromosomes, and the proportions of each passed on to progeny can vary as a result of cytoplas-mic segregation. The proportions in one person can also vary in different tissues or over time. The accumulation of certain types of mitochondrial mutations over time has been proposed as a possible cause of aging.

Figure 3-24 shows some of the mutations in human mitochondrial genes that can lead to disease when, by random drift and cytoplasmic segregation, they rise in frequency to such an extent that cell function is impaired. The inheritance of a human mitochondrial disease is shown in Figure 3-25. Note that the condition is always passed to offspring by mothers and never fathers. Occasionally, a mother will produce an unaffected child (not shown), probably owing to cyto-plasmic segregation in the gamete-forming tissue.

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Differences and similarities of homologous mtDNA sequences between species have been used extensively to construct evolutionary trees. Furthermore, it has been possible to introduce some extinct organisms into evolutionary trees using mtDNA sequences obtained from the remains of extinct organisms, such as skins and bones in museums. mtDNA evolves relatively rapidly, so this approach has been most useful in plotting recent evolution such as the evolution of humans and other primates. One key finding is that the “root” of the human mtDNA tree is in Africa, suggesting that Homo sapiens originated in Africa and from there dispersed throughout the world (see Chapter 18).

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