Organelles and the Molecular Biology of Eukaryotes Help (page 3)
Mitochondria vs. Chloroplasts
Mitochondria and chloroplasts have evolved for specialized functions in eukaryotic cells. Mitochondria are thought of as the powerhouse of the cell because many enzymes involved in cellular respiration and ATP production are located there. Chloroplasts serve as the site of photosynthesis in plants. Both mitochondria and chloroplasts share several characteristics with modern prokaryotic cells. All three generally have a circular double-stranded DNA genome (exceptions include some protozoans such as Paramecium and Tetrahymena that have linear mitochondrial DNA molecules). Their genomes are neither enclosed within a nuclear membrane nor associated with histone proteins (hence no nucleosome organization). They each code for part of their own protein-synthesizing systems (all rRNAs, tRNAs, and at least some of the ribosomal proteins). Many of the enzymes and other proteins that function in these organelles, however, are encoded by nuclear genes, synthesized on 80S ribosomes, and transported into these organelles. Their ribosomes are usually 70S or smaller and are sensitive to antibiotics and other substances that have no effect on the 80S eukaryotic cytoplasmic ribosomes. Protein synthesis is initiated by formyl-methionyl-tRNA. The nucleus, mitochondrion, and chloroplast are each bounded by a double-membrane envelope, but only the nuclear membrane contains pores. Mitochondria and chloroplasts grow in size and then seem to split in two, in a process akin to binary fission in bacteria.
Mitochondria are organelles found in the cytoplasm of both plants and animals. They contain the enzymes of the electron-transport chain that carry out oxidative phosphorylation in the production of adenosine triphosphate (ATP, the main source for energy-requiring biochemical reactions). Unlike chloroplasts, the mitochondrial genome (mtDNA) varies markedly in length between species. For example, in fungi, such as the yeast Saccharomyces cerevisiae, the mtDNA is about 86 kb, and inmostmetazoan (multicellular) animals it is on average 16 kb.Much of themtDNAof fungi and plants is thought to be noncoding (perhaps "junk" or "selfish" DNA). Animal mitochondrial genomes typically encode the same 37 proteins: 2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes. The proteins encoded are involved in respiration (i.e., cytochrome oxidase), DNA replication, transcription, and translation (e.g., ribosomal proteins). Mitochondrial genomes are also typically AT rich (~ 70%).
One or more mitochondrial DNA molecules resides within each of the several nucleoid regions within the mitochondrion. If a cell contains 250 mitochondria, each with 5 mtDNA molecules, there will be 1250 mtDNA copies in that cell. Mitochondrial ribosomes are also highly variable between species (e.g., 55S in animals, 73S in yeast). There is also some interspecific variation in mitochondrial tRNAs. Some codons are read differently by mitochondrial tRNAs than by nuclear-encoded tRNAs. For example, AUA codes for methionine (not isoleucine) andUGAcodes for tryptophan (not translation termination) inmammalian mitochondria. MitochondrialmRNAs of fungi and higher plants contain introns, but those of animals lack introns and are transcribed as polycistronic mRNAs that become cut into monocistronic mRNAs before translation. Mitochondria have no DNA repair systems. Hence, the mutation rate of mictochondrial DNA is much higher than that of nuclear DNA.
Chloroplasts contain the enzymes for photosynthesis and are thus characteristic only of plant cells. Most plant cells contain numerous chloroplasts. A few plants such as the unicellular alga Chlamydomonas (see Fig. 5-1) contain a single chloroplast. In most plants, however, each chloroplast genome is usually present in multiple copies. For example, a typical leaf cell of Euglena may contain 40–50 chloroplasts. Every chloroplast usually contains several nucleoid regions, each containing 8-10 DNA molecules; thus the entire cell may contain over 500 copies of the chloroplast genome (ctDNA). The length of a typical plant chloroplast genome is 120–150 kb of DNA. The number of protein-coding genes contained within ctDNA ranges from 46 to 90. The majority of these proteins are involved in photosynthesis, with the remainder being involved in replication, division, transcription, translation, and biosynthesis. There are also two genes for rRNAs and over 30 tRNA genes. Evidence indicates that ctDNA from liverworts to the higher plants have essentially the same genome (highly conserved). Some of the ctDNA genes (both for tRNAs and mRNAs) are known to contain introns. The RNA polymerase of the liverwort Marchantia polymorpha contains α- and β-subunits that are homologous in amino acid sequences to those found in the bacterium E. coli.
Origin of Organelles
Themost supported idea regarding the origin of organelles is the endosymbiosis or endosymbiont theory. This theory proposes that eukaryotic organelles arose as a result of symbiotic relationships between early bacterial cells. Several lines of evidence support the theory that mitochondria evolved from Eubacteria, or true bacteria, rather than the Archaea. According to the endosymbiosis theory, a primitive anaerobic-phagocytic type of nucleated cell (called the urkaryote) engulfed an aerobic bacterium (the progenote) that was able to generate energy by oxidative phosphorylation. The engulfed bacteriumsomehowescaped digestion and replicatedwithin the cytoplasm. These early symbiotic relationships gradually evolved into a mutualism whereby they could not survive apart from one another. During the evolution of this organelle, the bacteria gave upmany of its genes to the nucleus, so that nowmany of the proteins needed for mitochondrial functions are specified by nuclear genes, made on cytoplasmic ribosomes, and transported into the mitochondria. This is how fully aerobic, nucleated cells (like modern eukaryotic cells) are proposed to have evolved.
At some later time, some of these fully aerobic, nucleated cells may have engulfed photosynthetic cyanobacteria (blue-green "algae"). A mutualism gradually developed between these two entities in the evolution of the chloroplasts that characterize the plant kingdom.
There are no real clues in extant organisms as to the evolution of the nucleus. It is thought that the eukaryotic nuclear membrane probably evolved independently of the prokaryotes, possibly by invaginations and coalescences of the cell membrane. The nucleus is a double-membraned organelle like mitochondria and chloroplasts, so any theory regarding the origins of these organelles would have to take this into consideration.
Although the shape of mitochondria is different from that of the bacteria from which they presumably were derived, the mitochondria resemble bacteria in many ways. Both of their genomes are circular and histone-free. Their transcription and translation systems are also similar. On the other hand, some archaebacterial genes (like those in the eukaryote nucleus) have introns. But introns are unknown in modern Eubacteria. Hence, it has been suggested that the progenote may have had introns that were lost during the evolution of the Eubacteria. Interestingly, the mitochondrial DNA of mammalian cells does not contain introns, but many mitochondrial genomes of more primitive eukaryotes do. In addition, Eubacteria and eukaryotes contain ester-linked, unbranched lipids containing L-glycerophosphate, whereas the branched lipids of Archaebacteria are etherlinked and contain D-glycerophosphate. Finally, with the advent of DNA-sequencing technology, mitochondrial gene sequences can be compared with bacterial gene sequences. These investigations are showing that there is a high degree of relatedness between mtDNA genes and bacterial genes.
Inheritance of Organelles
In most plants and animals, mitochondria and chloroplasts are strictly inherited only from the female parent (maternal transmission) because the male gamete (or that part that enters into fertilization) is essentially devoid of these organelles. It is estimated that in about two-thirds of plant species the inheritance of chloroplasts is strictly maternal. Traits with an extranuclear basis may be identified on the basis of several diagnostic criteria.
- Differences in reciprocal crosses that cannot be attributed to sex linkage or some other chromosomal basis tend to implicate cytoplasmic factors.
- If progeny show only the characteristics of the female parent that can be attributed to unequal cytoplasmic contributions of male and female parents, then plasmagene inheritance is suspect (Example 13.24).
- If the uniparental inheritance of a trait cannot be attributed to unequal cytoplasmic contributions from the parents, this does not necessarily rule out cytoplasmic factors (Example 13.25).
- Extranuclear factors may be detected by either the absence of segregation at meiosis (Example 13.26) or by segregation that fails to follow Mendelian laws (Example 13.27).
- Repeated backcrossing of progeny to one of the parental types for several generations causes their chromosomal endowment to rapidly approach 100% that of the recurrent parental line. The persistence of a trait in the progeny, when the backcross parent exhibits an alternative character, may be considered evidence for plasmagene inheritance (Example 13.28).
EXAMPLE 13.24 In higher plants, pollen usually contributes very little, if any, cytoplasm to the zygote. Most of the cytoplasmic elements are transmitted through the maternal parent. In the plant called "four-o'clock" (Mirabilis jalapa), there may be normal green, pale green, and variegated branches due to two types of chloroplasts. Plants grown from seeds that developed on normal green branches (with all normal chloroplasts) will all be normal green; those that developed on pale-green branches (with abnormal chloroplasts) will all be pale green; those on variegated branches (with both normal and abnormal chloroplasts) will segregate green, pale green, and variegated in irregular ratios. The type of pollen used has no effect in this system. The irregularity of transmission from variegated branches is understandable if plasmagenes exist in the chloroplasts, because there is no mechanism to ensure the regular distribution of chloroplasts to daughter cells as there is for chromosomes.
EXAMPLE 13.25 The uniting gametes of the single celled alga Chlamydomonas reinhardi (Fig. 5-1) are morphologically indistinguishable. One strain of the alga that is streptomycin-resistant (sr) and of the "plus" mating type (mt+) is crossed to a cell of "negative" mating type (mt–) that is streptomycin-sensitive (ss). All progeny are resistant, but the nuclear genes for mating type segregate as expected: 1/2mt+, 1/2mt–. The reciprocal cross ss mt+ × sr mt–, again shows the expected segregation for mating type, but all progeny are sensitive. Repeated backcrossings of sr mt+ to ss mt– fail to show segregation for resistance. It appears as though the plasmagenes of the mt– strain become lost in a zygote of mt+. The mechanism that inactivates the plasmagenes of mt– in the zygote is not well understood.
EXAMPLE 13.26 Slow-growing yeast cells called
petites lack normal activity of the respiratory enzyme cytochrome oxidase associated with the mitochondria. Petites can be maintained indefinitely in vegetative cultures through budding, but can sporulate only if crossed to wild type. When a haploid neutral petite cell fuses with a haploid wild-type cell of opposite mating type, a fertile wild-type diploid cell is produced. Under appropriate conditions, the diploid cell reproduces sexually (sporulates). The four ascospores of the ascus (Fig. 6-4) germinate into cells with a 1 : 1 mating-type ratio (as expected for nuclear genes), but they are all wild type. The petite trait never appears again, even after repeated backcrossings of both mating types to petite. The mitochrondrial factors for petite are able to perpetuate themselves vegetatively, but are "swamped," lost, or permanently altered in the presence of wild-type factors. Neutral petite behaves the same in reciprocal crosses regardless of mating type, and in this respect is different from the streptomycinresistance factors in Chlamydomonas (see Example 13.25).
EXAMPLE 13.27 Another type of petite in yeast, called suppressive, may segregate, but in a manner different from chromosomal genes. When haploid suppressive petites are crossed to wild types and each zygote is grown vegetatively as a diploid strain, both petites and wild types may appear, but in frequencies that are hardly Mendelian, varying from 1 to 99% petites. Diploid wild type cells may sporulate producing only wild-type ascospores. By special treatment, all diploid zygotes can be made to sporulate. The majority of the ascospores thus induced germinate into petite clones. Some asci have 4, 3, 2, 1, or 0 petite ascospores, suggesting that environmental factors may alter their segregation pattern. Nuclear genes, such as mating type, maintain a 1 : 1 ratio in all asci.
EXAMPLE 13.28 The protoperithecial parent in Neurospora (Fig. 6-5) supplies the bulk of the extrachromosomal material of the sexually produced ascospores. Very slow spore germination characterizes one strain of this fungus. The trait exhibits differences in reciprocal crosses and maternal inheritance, and fails to segregate at meiosis. When the slow strain acts as protoperithecial parent and the conidial strain has normal spore germination, all the progeny are slow, but possess 50% of the nuclear genes of the conidial parent. Each generation is then backcrossed to the conidial parent, so that the F2 contains 75%, F3 contains 87.5%, etc., of nuclear genes of the conidial parent. After the fifth or sixth backcross, the nuclear genes are almost wholly those of the conidial parent, but the slow germination trait persists in all of the progeny.
Exceptions are known to the generalization that cytoplasmic factors are maternally inherited.
EXAMPLE 13.29 When a green strain of geranium (Pelargonium) is crossed to a strain with white-margined leaves, the progeny may have green, white, or white-margined leaves. Since the results of reciprocal crosses are the same, it has been hypothesized that plastids can be transmitted to offspring by both the male and female gametes. Cells that contain a mixture of plastid genomes are said to be heteroplasmic; those that contain only one type of plastid genome are called homoplasmic.
Notice that the F1 is coiled dextrally, not because its own genotype is s+/s, but because the maternal parent possessed the dominant dextral gene s+. Likewise in the first selfing generation, all are phenotypically dextral regardless of their own genotype because the F1 was s+/s. In the second selfing generation, we expect the following:
Practice problems for these concepts can be found at:
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