Non-nuclear Genes and Their Inheritance

Offspring inherit a combination of nuclear chromosomes from each of their parents as a result of fertilization. However, it turns out that some genes are passed on from parent to offspring without ever being part of a nuclear chromosome. Where are these genes found, and how does the transmission of such genes occur? Moreover, why do some of these genes appear to be inherited solely from the maternal parent, while others come solely from the paternal parent? The answer lies within cells' cytoplasm.

In 1909, not long after Mendel's principles of inheritance became well accepted, Carl Correns noticed some strange patterns of inheritance in four-o'clock plants, Mirabilis jalapa (Pierce, 2005; Correns, 1909). Specifically, the leaves and stems of these plants would sometimes appear variegated, meaning that instead of being a solid green color, they would occasionally show patches of green and white in a swirl-like pattern. Furthermore, within the same plants, branches might show a variety of leaf patterns. For example, while some of a plant's leaves would be variegated, others would be all green, and still others would be all white. During the course of his cross-pollination experiments with Mirabilis, Correns noticed that if a seed came from a solid green branch, it never produced variegated progeny, even if the pollen used for fertilization was from a flower on a variegated branch. In fact, no matter what type of leaf pattern existed on the branch that donated pollen, the seed would always produce leaves with the color pattern of the maternal plant branch. In addition, if the maternal branch was variegated, the progeny would appear with either green, white, or variegated leaves, but never in any predictable Mendelian ratio. Correns thus began to suspect that the maternal parent determined the phenotype of the offspring leaf color, because the paternal source of pollen never affected the outcome (Figure 1). In other words, Correns hypothesized that leaf color in Mirabilis was passed on via a uniparental mode of inheritance.

With modern DNA analysis techniques, scientists can actually trace inheritance by looking directly at markers on genes in parents and progeny after a test cross, rather than doing multiple backcrosses. In fact, exploring issues of heredity in this way can help us understand how organisms are related throughout evolution. And this is exactly what biologist A. K. Hansen and her colleagues were trying to understand when they used DNA screens to measure the inheritance of the chloroplast genome in different species of Passiflora (Hansen et al., 2007). Through their research, the team found that all interspecific crosses (crosses between species) had primarily paternal chloroplast inheritance, while nearly all intraspecific crosses (crosses within the same species) had primarily maternal inheritance. According to these results, mating outside the species is somehow detected at the germ cell level, and a choice is made to switch to paternal chloroplast inheritance.

However, one intraspecific cross really stood out among all others. In this cross, three out of 15 progeny showed biparental chloroplast inheritance, also known as heteroplasmy, while the remaining 12 showed maternal inheritance. Though it was (and still is) unclear how this heteroplasmy occurred, it was surprising that two modes of inheritance could exist simultaneously in the progeny of just one cross! The experiments of Hansen et al. have thus demonstrated that new rules about cytoplasmic inheritance emerge all the time.

Passiflora Species Crossed	Number of Progeny	Mode of Chloroplast Inheritance in Progeny
P. costaricensis x P. costaricensis (intraspecific)	15	12 maternal, 3 biparental
P. oerstedii x P. retipetala (interspecific)	17	17 paternal

(Table excerpted from Hansen et al., 2007)

Of course, chloroplasts are not the only DNA-containing organelle inherited through gamete cytoplasm. Mitochondria also contain DNA, and they show similar patterns of uniparental and biparental inheritance. In fact, because most animals lack chloroplasts, the main form of cytoplasmic inheritance in animals is via mitochondrial DNA, which is known as mtDNA.

The first people to capture images of DNA "fibers" in mitochondria were Margit and Sylvan Nass in 1963. With a powerful electron microscope, they were able to zoom in on part of a mitochondrion and take a photograph at a magnification of 150,000X. In doing so, the Nasses noticed a black threaded material inside mitochondria that would disappear after exposure to an enzyme (deoxyribonuclease) that specifically dissolved DNA. This was the first visual and chemical evidence that DNA existed in mitochondria.

Since the Nass experiments, interest in mtDNA has expanded greatly. Scientists now know that within a single cell, there can be thousands of mitochondria, and each mitochondrion contains from two to ten copies of mtDNA. During cell division, the mitochondria aggregate randomly into progeny cells. This means that each cell can theoretically contain a different mixture of normal mtDNA and mutated mtDNA, which can in turn generate a variety of phenotypes (Figure 2). But are these mtDNA mutations anything more than a sideshow to the main events of nuclear function? Indeed they are. Mutations in mitochondria can have very serious effects, and they are even the basis for several diseases. Mitochondria's crucial role as the main producer of ATP within cells means that malfunctions in these organelles are truly bad news.

Extranuclear inheritance of mitochondria has been tracked in families that carry defective mitochondrial genes. Some of the diseases caused by defective mitochondria particularly affect muscle tissue, as muscle uses ATP and mitochondria are cellular producers of this substance. One such condition is an inherited disorder called progressive external ophthalmoplegia (PEO). Spelbrink et al. (2001) analyzed multiple pedigrees of families affected by PEO, and they analyzed the mitochondrial genes along with the inheritance pattern of the disease. Eventually, the researchers noticed that the mtDNA of those individuals affected with PEO showed many more deleted sequences than the mtDNA of unaffected individuals. Next, the team tried to figure out what these deletions meant for mitochondrial function. After taking blood samples from 12 different families affected with PEO, they extracted mtDNA from blood lymphocytes and screened it for common patterns in affected and unaffected individuals. They found that PEO carriers had 11 different deletions in the coding sequence for a mitochondrial protein that appeared to be involved in mtDNA replication. They named this protein Twinkle, because it is distributed all over mitochondria like a constellation pattern in the night sky. The investigators concluded that Twinkle is likely a DNA helicase protein involved in maintaining the integrity of mtDNA as it replicates. Therefore, although Twinkle is encoded by nuclear DNA, it affects the transcription of mtDNA (Spelbrink et al., 2001). In other words, when it comes to PEO, both nuclear and mitochondrial DNA are involved in the inheritance of a single disease.

At first glance, the inheritance of nonnuclear genes appears to follow a random pattern of cytoplasmic matter separation. But as we examine this mode of inheritance more closely, new patterns emerge that betray that far more complex processes affect the transfer and maintenance of the organelle genome. It has also become clear that mtDNA may have a close relationship with nuclear genes, and that the integrity of mtDNA may be related to actions coordinated by the cell nucleus.

Overall, nonnuclear inheritance is characterized by random patterns of distribution in progeny that appear to follow an entirely different set of rules we are only beginning to understand. In fact, some inheritance patterns are not always due strictly to DNA, nuclear or otherwise. For example, the direction of coiling in snails is determined by a nonuniform distribution of cytoplasmic factors in the early embryo. Early cell divisions result in irregular distribution of these factors in the embryonic cells, which has been linked to the inheritance of left- or right-handed coiling (Gilbert, 2006).

Together, all cellular sources of DNA and the intracellular factors that are inherited from parent to offspring interact to influence the heredity of traits. The complexity of all these parts working together makes inheritance relevant even today. Mendelian principles helped guide the way for understanding the basic inheritance of alleles, but the complexity of how genetic, epigenetic, and environmental factors intertwine to control distinct phenotypes continues to be explored by scientists every day.