11.4 Organelle DNA Has Unique Characteristics

As we have seen, eukaryotic chromosomes reside within the nucleus and have a complex structure consisting of DNA and associated histone proteins. However, some DNA found in eukaryotic cells occurs outside the nucleus, has a very different organization, and exhibits a different pattern of inheritance from nuclear DNA. This DNA occurs in mitochondria and chloroplasts, which are membrane-bounded organelles located in the cytoplasm of eukaryotic cells (Figure 11.11).

Figure 11.11: Comparison of the structures of mitochondria and chloroplasts.
[Left: Don W. Fawcett/Science Source/Photo Researchers, Inc. Right: Biophoto Associates/Photo Researchers.]

Mitochondrion and Chloroplast Structure

Mitochondria are present in almost all eukaryotic cells, whereas chloroplasts are found in plants and some protists. Both organelles generate ATP, the universal energy carrier of cells.

Mitochondria are tubular structures that are from 0.5 to 1.0 micrometer (μm) in diameter, about the size of a typical bacterium, whereas chloroplasts are typically from about 4 to 6 mm in diameter. Both are surrounded by two membranes enclosing a region (called the matrix in mitochondria and the stroma in chloroplasts) that contains enzymes, ribosomes, RNA, and DNA. In mitochondria, the inner membrane is highly folded; embedded within it are the enzymes that catalyze electron transport and oxidative phosphorylation. Chloroplasts have a thylakoid membrane, which is highly folded and stacked to form aggregates called grana. This membrane bears the pigments and enzymes required for photophosphorylation. New mitochondria and chloroplasts arise by the division of existing organelles—divisions that take place throughout the cell cycle and are independent of mitosis and meiosis.

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Mitochondria and chloroplasts possess DNA that encodes some polypeptides used by the organelle, as well as RNA found in the ribosome (ribosomal RNA or rRNA) and some transfer RNAs (tRNAs) needed for the translation of these proteins. The genes for most of the 900 or so structural proteins and enzymes found in mitochondria are actually encoded by nuclear DNA; the mitochondrial genome typically encodes only a few proteins and a few rRNA and tRNA molecules needed for mitochondrial protein synthesis.

The Endosymbiotic Theory

Chloroplasts and mitochondria are similar to bacteria in many ways. This resemblance is not superficial; indeed there is compelling evidence that these organelles evolved from eubacteria. The endosymbiotic theory (Figure 11.12) proposes that mitochondria and chloroplasts were once free-living bacteria that became internal inhabitants (endosymbionts) of early eukaryotic cells. It is assumed that over evolutionary time, many of the endosymbiont’s original genes were subsequently lost (because nuclear genes existed that provided the same function) or were transferred to the nucleus.

Figure 11.12: The endosymbiotic theory proposes that mitochondria and chloroplasts in eukaryotic cells arose from eubacteria.

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A great deal of evidence supports the idea that mitochondria and chloroplasts originated as eubacterial cells. Many modern single-celled eukaryotes (protists) are hosts to endosymbiotic bacteria. Mitochondria and chloroplasts are similar in size to present-day eubacteria and possess their own DNA, which has many characteristics in common with eubacterial DNA. Mitochondria and chloroplasts possess ribosomes, some of which are similar in size and structure to eubacterial ribosomes. In addition, antibiotics that inhibit protein synthesis in eubacteria but do not affect protein synthesis in eukaryotic cells also inhibit protein synthesis in these organelles.

The strongest evidence for the endosymbiotic theory comes from the study of DNA sequences, which demonstrate that sequences in mtDNA and cpDNA are more closely related to sequences in the genes of eubacteria than they are to those found in the eukaryotic nucleus. All of this evidence indicates that mitochondria and chloroplasts are more closely related to eubacterial cells than they are to the eukaryotic cells in which they are now found.

CONCEPTS

Mitochondria and chloroplasts are membrane-bounded organelles of eukaryotic cells that generally possess their own DNA. The well-supported endosymbiotic theory proposes that these organelles began as free-living eubacteria that developed stable endosymbiotic relations with early eukaryotic cells.

CONCEPT CHECK 8

What evidence supports the endosymbiotic theory?

Uniparental Inheritance of Organelle-Encoded Traits

Mitochondria and chloroplasts are present in the cytoplasm, as already stated, and are usually inherited from a single parent. Thus, traits encoded by mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) exhibit uniparental inheritance (see Chapter 5). In animals, mtDNA is inherited almost exclusively from the female parent, although occasional male transmission of mtDNA has been documented. Maternal inheritance of animal mtDNA may be partly a function of gamete size—sperm are much smaller than eggs and hold fewer mitochondria. However, recent research has found that in some eukaryotes, paternal mitochondria are selectively eliminated by autophagy, a process in which mitochondria are digested by the cell. Paternal mitochondria are targeted for destruction, whereas maternal mitochondria are not; the mechanism that produces this difference is not known. Paternal inheritance of organelles is common in gymnosperms (conifers) and in a few angiosperms (flowering plants). Some plants even exhibit biparental inheritance of mtDNA and cpDNA.

Replicative Segregation

Individual cells may contain from dozens to hundreds of organelles, each with numerous copies of the organelle genome, so each cell typically possesses from hundreds to thousands of copies of mitochondrial and chloroplast genomes (Figure 11.13). A mutation arising within one organelle DNA molecule generates a mixture of organelles within the cell, some with a mutant DNA sequence and others with a wild-type DNA sequence. The occurrence of two distinct varieties of DNA within the cytoplasm of a single cell is termed heteroplasmy. When a heteroplasmic cell divides, the organelles segregate randomly into the two progeny cells in a process called replicative segregation (Figure 11.14), and chance determines the proportion of mutant organelles in each cell. Although most progeny cells will inherit a mixture of mutant and normal organelles, just by chance some cells may receive organelles with only mutant or only wild-type sequences; this situation, in which all organelles are genetically identical, is known as homoplasmy. Fusion of mitochondria also takes place frequently.

Figure 11.13: Individual cells may contain many mitochondria, each with several copies of the mitochondrial genome. Shown is a cell of Euglena gracilis, a protist, stained so that the nucleus appears red, mitochondria green, and mtDNA yellow.
[From Y. Huyashi and K. Veda, Journal of Cell Sciences 93:565, 1989.]
Figure 11.14: Organelles in a heteroplasmic cell divide randomly into the progeny cells. This diagram illustrates replicative segregation in mitosis; the same process also takes place in meiosis.

When replicative segregation takes place in somatic cells, it may create phenotypic variation within a single organism; different cells of the organism may possess different proportions of mutant and wild-type sequences, resulting in different degrees of phenotypic expression in different tissues. When replicative segregation takes place in the germ cells of a heteroplasmic cytoplasmic donor there may be different phenotypes among the offspring.

The disease known as myoclonic epilepsy and ragged red fiber syndrome (MERRF) is caused by a mutation in an mtDNA gene. A 20-year-old person who carried this mutation in 85% of his mtDNAs displayed a normal phenotype, whereas a cousin who had the mutation in 96% of his mtDNAs was severely affected. In diseases caused by mutations in mtDNA, the severity of the disease is frequently related to the proportion of mutant mtDNA sequences inherited at birth. TRY PROBLEM 28

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Traits Encoded By mtDNA

A number of traits affected by organelle DNA have been studied. One of the first to be examined in detail was the phenotype produced by petite mutations in yeast (Figure 11.15). In the late 1940s, Boris Ephrussi and his colleagues noticed that, when grown on solid medium, some colonies of yeast were much smaller than normal. Examination of these petite colonies revealed that the growth rates of the cells within the colonies were greatly reduced. The results of biochemical studies demonstrated that petite mutants were unable to carry out aerobic respiration; they obtained all of their energy from anaerobic metabolism (glycolysis and fermentation), which is much less efficient than aerobic respiration and results in the smaller colony size.

Figure 11.15: The petite mutants have large deletions in their mtDNA and are unable to carry out oxidative phosphorylation. Colonies of normal yeast cells and colonies of petite mutants.
[From Xin Jie Chen and G. Desmond Clark-Walker, Genetics 144: 1445–1454, Fig1, 1996. © Genetics Society of America. Courtesy of Xin Jie Chen, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University.]

Some petite mutations are defects in nuclear DNA, but most petite mutations occur in mitochondrial DNA. Mitochondrial petite mutants often have large deletions in mtDNA or, in some cases, are missing mtDNA entirely. Much of the mtDNA encodes enzymes that catalyze aerobic respiration; therefore the petite mutants are unable to carry out aerobic respiration and cannot produce normal quantities of ATP, which inhibits their growth.

Another known mtDNA mutation occurs in Neurospora. Isolated by Mary Mitchell in 1952, poky mutants grow slowly, display cytoplasmic inheritance, and have abnormal amounts of cytochromes. Cytochromes are protein components of the electron-transport chain of the mitochondria and play an integral role in the production of ATP. Most organisms have three primary types of cytochromes: cytochrome a, cytochrome b, and cytochrome c. Poky mutants have cytochrome c but no cytochrome a or b. Like petite mutants, poky mutants are defective in ATP synthesis and therefore grow more slowly than do normal, wild-type cells. TRY PROBLEM 32

In recent years, a number of genetic diseases that result from mutations in mtDNA have been identified in humans. In addition to MERRF syndrome mentioned earlier, Leber hereditary optic neuropathy (LHON) results from mutations in the mtDNA genes that encode electron-transport proteins. LHON typically leads to sudden loss of vision in middle age. Another disease caused by mtDNA mutations is neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP), which is characterized by seizures, dementia, and developmental delay. Other mitochondrial diseases include Kearns–Sayre syndrome (KSS) and chronic external opthalmoplegia (CEOP), both of which result in paralysis of the eye muscles, droopy eyelids, and, in severe cases, vision loss, deafness, and dementia. All of these diseases exhibit cytoplasmic inheritance and variable expression (see Chapter 5).

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A trait in plants that is produced by mutations in mitochondrial genes is cytoplasmic male sterility, a mutant phenotype found in more than 140 different plant species and inherited only from the maternal parent. These mutations inhibit pollen development but do not affect female fertility.

A number of cpDNA mutants also have been discovered. One of the first to be recognized was leaf variegation in the four o’clock plant Mirabilis jalapa, which was studied by Carl Correns in 1909. In the green alga Chlamydomonas, streptomycin-resistant mutations occur in cpDNA, and a number of mutants exhibiting altered pigmentation and growth in higher plants have been traced to defects in cpDNA.

CONCEPTS

In most organisms, genes encoded by mtDNA and cpDNA are inherited from a single parent. A gamete may contain more than one distinct type of mtDNA or cpDNA; in these cases, random segregation of the organelle DNA may produce phenotypic variation within a single organism or it may produce different degrees of phenotypic expression among progeny.

CONCEPT CHECK 9

In a few organisms, traits encoded by mtDNA can be inherited from either parent. This observation indicates that in these organisms

  1. mitochondria do not exhibit replicative segregation.
  2. heteroplasmy is present.
  3. both sperm and eggs contribute cytoplasm to the zygote.
  4. there are multiple copies of mtDNA in each cell.

WORKED PROBLEM

To illustrate the inheritance of a trait encoded by organelle DNA, consider the following problem. A physician examines a young man who has a progressive muscle disorder and visual abnormalities. A number of the patient’s relatives have the same condition, as shown in the adjoining pedigree. The degree of expression of the trait is highly variable among members of the family: some are only slightly affected, whereas others developed severe symptoms at an early age. The physician concludes that this disorder is due to a mutation in the mitochondrial genome. Do you agree with the physician’s conclusion? Why or why not? Could the disorder be due to a mutation in a nuclear gene? Explain your reasoning.

Solution Strategy

What information is required in your answer to the problem?

An explanation of whether this disorder could be due to a mutation in the mitochondrial genome and why, as well as whether the disorder could be due to a mutation in a nuclear gene and why.

What information is provided to solve the problem?

  • The young man has a progressive muscle disorder and visual abnormalities.
  • A pedigree illustrating the young man’s family.
  • The trait is highly variable among members of the family.

Solution Steps

The conclusion that the disorder is caused by a mutation in the mitochondrial genome is supported by the pedigree and the observation of variable expression in affected members of the same family. The disorder is passed only from affected mothers to both male and female offspring; when fathers are affected, none of their children have the trait (as seen in the children of II-2 and III-6). This outcome is expected of traits determined by mutations in mtDNA, because mitochondria are in the cytoplasm and usually inherited only from a single (in humans, the maternal) parent. The trait cannot be X-linked recessive, because a cross between a female with the trait (XaXa) and a male without the trait (X+Y) would not produce daughters with the trait (XaXa), which we see in III-10, IV-3, and IV-4. It cannot be X-linked dominant because II-2 and III-6 would have to pass it to their daughters, who are unaffected (unless the trait exhibited incomplete penetrance).

The facts that some offspring of affected mothers do not show the trait (III-9 and IV-5) and that expression varies from one person to another suggest that affected persons are heteroplasmic, with both mutant and wild-type mitochondria. Random segregation of mitochondria in meiosis may produce gametes having different proportions of mutant and wild-type sequences, resulting in different degrees of phenotypic expression among the offspring. Most likely, symptoms of the disorder develop when some minimum proportion of the mitochondria are mutant. Just by chance, some of the gametes produced by an affected mother contain few mutant mitochondria and result in offspring that lack the disorder.

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Another possible explanation for the disorder is that it results from an autosomal dominant gene. When an affected (heterozygous) person mates with an unaffected (homozygous) person, about half of the offspring are expected to have the trait, but, just by chance, some affected parents will have no affected offspring. Individuals II-2 and III-6 in the pedigree could just have happened to be male and their sex could be unrelated to the mode of transmission. The variable expression could be explained by variable expressivity (see Chapter 5).

For more experience with the inheritance of organelle encoded traits, try working Problem 29 at the end of the chapter.

The Mitochondrial Genome

In most animals and fungi, the entire mitochondrial genome exists on a single, highly coiled, circular DNA molecule, although there may be many copies of this genome in each cell. The circular structure of the mitochondria is similar in structure to a eubacterial chromosome. Plant mitochondrial genomes often exist as a complex collection of multiple circular DNA molecules. In some species, the mitochondrial genome consists of a single, linear DNA molecule.

Each mitochondrion contains multiple copies of the mitochondrial genome, and a cell may contain many mitochondria. A typical rat liver cell, for example, has from 5 to 10 mtDNA molecules in each of about 1000 mitochondria; so each cell possesses from 5000 to 10,000 copies of the mitochondrial genome. Mitochondrial DNA constitutes about 1% of the total cellular DNA in a rat liver cell. Like eubacterial chromosomes, mtDNA lacks the histone proteins normally associated with eukaryotic nuclear DNA, although it is complexed with other proteins that have some histone-like properties. The guanine–cytosine (GC) content of mtDNA is often sufficiently different from that of nuclear DNA in that mtDNA can be separated from nuclear DNA by density-gradient centrifugation.

Mitochondrial genomes are small compared with nuclear genomes and vary greatly in size among different organisms (Table 11.4). The sizes of mitochondrial genomes of most species range from 15,000 bp to 65,000 bp, but those of a few species are much smaller (e.g., the genome of Plasmodium falciparum, the parasite that causes malaria, is only 6,000 bp) while those of some plants are several million base pairs. Although the amount of DNA in mitochondrial genomes varies widely, there is no correlation between genome size and number of genes. The number of genes is more constant than genome size; most species have only from 40 to 50 genes. These genes encode five basic functions: respiration and oxidative phosphorylation, translation, transcription, RNA processing, and the import of proteins into the cell. Most of the variation in size of mitochondrial genomes is due to differences in noncoding DNA sequences. As mentioned earlier, genes for most of the proteins and enzymes found in mitochondria are actually encoded by nuclear DNA.

Organism Size of mtDNA (bp)
Pichia canadensis (fungus) 27,694
Podospora anserina (fungus) 100,314
Saccharomyces cerevisiae (fungus) 85,779*
Drosophila melanogaster (fruit fly) 19,517
Lumbricus terrestris (earthworm) 14,998
Xenopus laevis (frog) 17,553
Mus musculus (house mouse) 16,295
Homo sapiens (human) 16,569
Chlamydomonas reinhardtii (green alga) 15,758
Plasmodium falciparum (protist) 5,966
Paramecium aurelia (protist) 40,469
Arabidopsis thaliana (plant) 166,924
Cucumis melo (plant) 2,400,000
*Size varies among strains.
Table : Table 11.4: Sizes of mitochondrial genomes in selected organisms

Human mtDNA

Human mtDNA is a circular molecule encompassing 16,569 bp that encode two rRNAs, 22 tRNAs, and 13 proteins. The two nucleotide strands of the molecule differ in their base composition: the heavy (H) strand has more guanine nucleotides, whereas the light (L) strand has more cytosine nucleotides. The H strand is the template for both rRNAs, 14 of the 22 tRNAs, and 12 of the 13 proteins, whereas the L strand serves as template for only 8 of the tRNAs and 1 protein. The D loop (Figure 11.16) is a region of the mtDNA that contains sites where replication and transcription of the mtDNA is initiated. Human mtDNA is highly economical in its organization: there are few noncoding nucleotides between the genes and almost all the messenger RNA codes for proteins. Human mtDNA also contains very little repetitive DNA. The one region of the human mtDNA that does contain some noncoding nucleotides is the D loop.

Figure 11.16: The human mitochondrial genome, consisting of 16,569 bp, is highly economical in its organization. (a) The outer circle represents the heavy (H) strand, and the inner circle represents the light (L) strand. The origins of replication for the H and L strands are ori H and ori L, respectively. ND identifies genes that encode subunits of NADH dehydrogenase. (b) Electron micrograph of isolated mtDNA.
[Part b: CNRI/Photo Researchers.]

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Yeast mtDNA

The organization of yeast mtDNA is quite different from that of human mtDNA. Although the yeast mitochondrial genome with 78,000 bp is nearly five times as large, it encodes only six additional genes, for a total of 2 rRNAs, 25 tRNAs, and 16 polypeptides (Figure 11.17). Most of the extra DNA in the yeast mitochondrial genome consists of noncoding sequences found within and between genes.

Figure 11.17: The yeast mitochondrial genome, consisting of 78,000 bp, contains much noncoding DNA.

Flowering-Plant mtDNA

Flowering plants (angiosperms) have the largest and most-complex mitochondrial genomes known; their mitochondrial genomes range in size from 186,000 bp in white mustard to 2,400,000 bp in musk-melon. Even closely related plant species may differ greatly in the sizes of their mtDNA.

Part of the extensive size variation in the mtDNA of flowering plants can be explained by the presence of long sequences that are direct repeats. Crossing over between these repeats can generate multiple circular chromosomes of different sizes. The mitochondrial genome in turnips, for example, consists of a “master circle” consisting of 218,000 bp that has direct repeats. Homologous recombination between the repeats can generate two smaller circles of 135,000 bp and 83,000 bp (Figure 11.18). Other species contain several direct repeats, providing possibilities for complex crossing-over events that may increase or decrease the number and sizes of the circles.

Figure 11.18: Size variation in plant mtDNA can be generated through recombination between direct repeats. In turnips, the mitochondrial genome consists of a “master circle” of 218,000 bp; crossing over between the direct repeats produces two smaller circles of 135,000 bp and 83,000 nucleotide pairs.

CONCEPTS

The mitochondrial genome consists of circular DNA with no associated histone proteins, although it is complexed with other proteins that have some histone-like properties. The sizes and structures of mtDNA differ greatly among organisms. Human mtDNA exhibits extreme economy, but mtDNAs found in yeast and flowering plants contain many noncoding nucleotides and repetitive sequences. Mitochondrial DNA in most flowering plants is large and typically has one or more large direct repeats that can recombine to generate smaller or larger molecules.

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The Evolution of Mitochondrial DNA

As already mentioned, comparisons of mitochondrial DNA sequences with DNA sequences in bacteria strongly support a common eubacterial origin for all mtDNA. Nevertheless, patterns of evolution seen in mtDNA vary greatly among different groups of organisms.

The sequences of vertebrate mtDNA exhibit an accelerated rate of evolution: the sequences in mammalian mtDNA, for example, typically change from 5 to 10 times as fast as those in mammalian nuclear DNA. The accelerated rate of evolution seen in vertebrate mtDNA is due to its high mutation rate, which allows DNA sequences to change more quickly. In spite of the high rate of sequence evolution, the number of genes present and the organization of vertebrate mitochondrial genomes are relatively constant. In contrast, sequences of plant mtDNA evolve slowly at a rate only that of the nuclear genome, but their gene content and organization change rapidly. The reason for these basic differences in rates of evolution is not yet known.

Mitochondrial DNA has been studied extensively to reconstruct patterns of evolution in humans and many other organisms. Some of the advantages of mtDNA for studying evolution include: (1) the small size and abundance of mtDNA in the cell; (2) the rapid evolution of mtDNA sequences in some organisms, facilitating study of closely related groups; and (3) the maternal inheritance of mtDNA and lack of recombination, which makes it possible to trace female lines of descent. Samples of human mtDNA have been analyzed from thousands of people belonging to hundreds of different ethnic groups throughout the world. These mtDNA samples are helping to unravel many aspects of human evolution and history. For example, initial studies on mtDNA sequences led to the proposal that small groups of humans migrated out of Africa about 85,000 years ago and populated the rest of the world. This is called the Out of Africa hypothesis or the African Replacement hypothesis, and has now gained wide acceptance. The Out of Africa hypothesis is supported by additional studies of DNA sequences from the Y chromosome and nuclear genes. The use of mtDNA in evolutionary studies will be described in more detail in Chapter 26.

At conception, a mammalian zygote inherits approximately 100,000 copies of mtDNA inherited from the egg. Because of the large number of mtDNA molecules in each cell and the high rate of mutation in mtDNA, most cells would be expected to contain a mixture of wild-type and mutant mtDNA molecules (heteroplasmy). However, heteroplasmy is rarely present: in most organisms, the copies of mtDNA are genetically identical (homoplasmy). To account for the uniformity of mtDNA within individual organisms, geneticists hypothesize that, in early development or gamete formation, mtDNA goes through some type of bottleneck, during which the mtDNAs within a cell are reduced to just a few copies, which then replicate and give rise to all subsequent copies of mtDNA. Through this process, genetic variation in mtDNA within a cell is eliminated and most copies of mtDNA are identical. Recent studies have provided evidence that a bottleneck does exist, but there is contradictory evidence concerning where in development it arises.

CONCEPTS

All mtDNA appears to have evolved from a common eubacterial ancestor, but the patterns of evolution seen in different mitochondrial genomes vary greatly. Vertebrate mtDNA exhibits rapid change in sequence but little change in gene content and organization, whereas the mtDNA of plants exhibits little change in sequence but much variation in gene content and organization. Mitochondrial DNA sequences are frequently used to study patterns of evolution.

Damage to Mitochondrial DNA Is Associated with Aging

The symptoms of many human genetic diseases caused by defects in mtDNA first appear in middle age or later and increase in severity as people age. One hypothesis to explain this is related to the decline in oxidative phosphorylation with aging.

Oxidative phosphorylation is the process that generates ATP, the primary carrier of energy in the cell. This process takes place on the inner membrane of the mitochondrion and requires a number of different proteins, some encoded by mtDNA and others encoded by nuclear genes. Oxidative phosphorylation normally declines with age and, if it falls below a critical threshold, tissues do not make enough ATP to sustain vital functions and disease symptoms appear. Most people start life with an excess capacity for oxidative phosphorylation; this capacity decreases with age, but most people reach old age or die before the critical threshold is passed. Persons born with mitochondrial diseases carry mutations in their mtDNA that lower their oxidative phosphorylation capacity. At birth, their capacity may be sufficient to support their ATP needs but, as their oxidative phosphorylation capacity declines with age, they cross the critical threshold and begin to experience disease symptoms.

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Why does oxidative phosphorylation capacity decline with age? A possible explanation is that damage to mtDNA accumulates with age: deletions and base substitutions in mtDNA increase with age. For example, a common 5000-bp deletion in mtDNA is absent in normal heart muscle cells before the age of 40, but, afterward, this deletion is present with increasing frequency. The same deletion is found at a low frequency in normal brain tissue before age 75 but is found in 11% to 12% of mtDNAs in the basal ganglia by age 80. People with mtDNA genetic diseases may age prematurely because they begin life with damaged mtDNA.

The mechanism of age-related increases in mtDNA damage is not yet known. Oxygen radicals—highly reactive compounds that are natural by-products of oxidative phosphorylation—are known to damage DNA. Because mtDNA is physically close to the enzymes taking part in oxidative phosphorylation, mtDNA may be more prone to oxidative damage than is nuclear DNA. When mtDNA has been damaged, the cell’s capacity to produce ATP drops.

The Chloroplast Genome

Geneticists have long recognized that many traits associated with chloroplasts exhibit cytoplasmic inheritance, indicating that these traits are not encoded by nuclear genes. In 1963, chloroplasts were shown to have their own DNA (Figure 11.19).

Figure 11.19: Chloroplast DNA of rice.

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Among different plants, the chloroplast genome ranges in size from 80,000 to 600,000 bp, but most chloroplast genomes range from 120,000 to 160,000 bp (Table 11.5). Chloroplast DNA is usually a single, double-stranded DNA molecule that is circular, highly coiled, and lacks associated histone proteins. As in mtDNA, multiple copies of the chloroplast genome are found in each chloroplast, and there are multiple organelles per cell; so there are several hundred to several thousand copies of cpDNA in a typical plant cell.

Organism Size of cpDNA (bp)
Euglena gracilis (protist) 143,172
Porphyra purpurea (red alga) 191,028
Chlorella vulgaris (green alga) 150,613
Marchantia polymorpha (liverwort) 121,024
Nicotiana tabacum (tobacco) 155,939
Zea mays (corn) 140,387
Pinus thunbergii (black pine) 119,707
Table : Table 11.5: Sizes of chloroplast genomes in selected organisms

The chloroplast genomes from a number of plant and algal species have been sequenced, and cpDNA is now recognized to be basically eubacterial in its organization: the order of some groups of genes is the same as that observed in E. coli, and many chloroplast genes are organized into clusters similar to those found in bacteria. Many of the sequences in cpDNA are quite similar to those found in equivalent eubacterial genes.

Among vascular plants, chloroplast chromosomes are similar in gene content and gene order. A typical chloroplast genome encodes 4 rRNA genes, from 30 to 35 tRNA genes, a number of ribosomal proteins, many proteins engaged in photosynthesis, and several proteins having roles in nonphotosynthetic processes. A key protein encoded by cpDNA is ribulose-1,5-bisphosphate carboxylase-oxygenase (abbreviated RuBisCO), which participates in the fixation of carbon in photosynthesis. RuBisCO makes up about 50% of the protein found in green plants and is therefore considered the most abundant protein on Earth. It is a complex protein consisting of eight identical large subunits and eight identical small subunits. The large subunit is encoded by chloroplast DNA, whereas the small subunit is encoded by nuclear DNA. Much of cpDNA consists of noncoding sequences.

The Evolution of Chloroplast DNA

The DNA sequences of chloroplasts are very similar to those found in cyanobacteria (a group of photosynthetic bacteria), so chloroplast genomes clearly have a eubacterial ancestry. Overall, cpDNA sequences evolve slowly compared with sequences in nuclear DNA and some mtDNA. For most chloroplast genomes, size and gene organization are similar, although there are some notable exceptions. Because they evolve slowly and, like mtDNA, are inherited from only one parent, cpDNA is often useful for determining the evolutionary relationships among different plant species.

CONCEPTS

Most chloroplast genomes consist of a single circular DNA molecule not complexed with histone proteins. Although there is considerable size variation among species, the cp-DNAs found in most vascular plants are about 150,000 bp. Chloroplast DNA sequences are most similar to DNA sequences in cyanobacteria, which supports the endosymbiotic theory.

CONCEPT CHECK 10

In its organization, chloroplast DNA is most similar to

  1. eubacteria.
  2. archaea.
  3. nuclear DNA of plants.
  4. nuclear DNA of primitive eukaryotes.

Through Evolutionary Time, Genetic Information Has Moved Between Nuclear, Mitochondrial, and Chloroplast Genomes

Many proteins found in modern mitochondria and chloroplasts are encoded by nuclear genes, which suggests that much of the original genetic material in the endosymbiont has probably been transferred to the nucleus. This assumption is supported by the observation that some DNA sequences normally found in mtDNA have been detected in the nuclear DNA of some strains of yeast and maize. Likewise, chloroplast sequences have been found in the nuclear DNA of spinach. Furthermore, the sequences of nuclear genes that encode organelle proteins are most similar to their eubacterial counterparts.

There is also evidence that genetic material has moved from chloroplasts to mitochondria. For example, DNA fragments from some rRNA genes that are normally encoded by cpDNA have been found in the mtDNA of maize. Sequences from the gene that encodes the large subunit of RuBisCO, which is normally encoded by cpDNA, are duplicated in maize mtDNA. And there is even evidence that some nuclear genes have moved into mitochondrial genomes. The exchange of genetic material between the nuclear, mitochondrial, and chloroplast genomes has given rise to the term “promiscuous DNA” to describe this phenomenon. The mechanism by which this exchange takes place is not entirely clear.

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