Uniparental inheritance of mitochondrial and chloroplast genes mechanisms and evolution

Introduction

When offspring inherit their genotype from only one parent, this is known as uniparental inheritance. This term can be applied to a wide range of genetic events, some examples of which are given below. Much of what follows addresses uniparental inheritance in diploid organisms. Uniparental inheritance in plants will not be considered here. Nonetheless, a substantial proportion of the earth’s biomass is composed of organisms with a predominantly haploid life cycle such as fungi and algae and these deserve a mention. For example, the fission yeast Schizosaccharomyces pombe normally reproduces asexually during vegetative growth, thus propagating the haploid state by uniparental inheritance. This yeast is also, however, capable of sexual reproduction to produce diploid cells. In response to starvation, these diploids will sporulate and give rise to haploid cells again by meiosis. When nutrients are plentiful, budding yeast strains such as the baker’s yeast Saccharomyces cerevisiae prefer to proliferate as diploid cells. On starvation, they too will undergo meiosis and can subsequently proliferate either asexually as haploids or sexually by mating with cells of the opposite mating type to form diploids. Yeast haploids are a valuable genetic tool for the identification and analysis of mutant genes in key cellular pathways such as cell cycle control. In the life cycle of the unicellular freshwater alga, Chlamydomonas, uniparental inheritance is evident through the asexual reproductive activity of the haploid cells. Once again in adverse environmental conditions, some of these cells are transformed into gametes and a pair fuses to form a diploid zygote. In favorable conditions after this sexual phase, meiosis occurs which gives rise to a new haploid generation.

Mitochondria are organelles that occupy a substantial cytoplasmic portion of the eukaryotic cell. They are responsible for completing the energy conversion used to drive cellular reactions. These organelles contain DNA which in mammals is about 10−5 times the size of the nuclear genome and are capable of carrying out their own DNA replication, transcription, and protein synthesis. The mitochondrial genome in humans encodes transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), and 13 other polypeptides. Mitochondrial genes undergo non-Mendelian cytoplasmic inheritance which, in higher mammals, is uniparental because the egg contributes much more cytoplasm to the zygote than does the sperm. Hence, this uniparental inheritance is maternal in origin.

Mammalian Cloning

A clone is any collection of cells that are descendants of a single ancestor cell. In the case of the cloning of a whole complex organism, that single ancestor is usually an enucleated egg which, instead of being fertilized, has received a diploid nucleus from a somatic cell. This can be considered as another form of uniparental inheritance as offspring are produced asexually without a contribution from two parents. Such nuclear transplantations in vertebrates were carried out in frogs in the 1980s in order to test the ability of nuclei from differentiated cells to support normal development. These studies, which addressed the question of whether irreversible changes in genes accompany differentiation, resulted in development to adulthood in a small number of cases. In general, in frogs, the later the developmental stage of the nucleus used, the more limited the developmental potential of the embryo. These studies suggested that there was limited reversibility of the differentiated state.

Until recently, mammalian cloning from fully differentiated cell types was even less successful. In cattle and sheep, a series of technical advances allowed transplanted nuclei from undifferentiated embryonic cells to give rise to viable offspring. More recently, donor nuclei from differentiated adult cells were also found to be capable of making a sheep clone after nuclear transplantation into an egg. This significant result indicates that the differentiated mammalian genome can be ‘reprogrammed’ to support development. This approach has now been used to produce mouse clones at a frequency of about 2% from adult somatic cell nuclei injected into enucleated eggs. The frequency of successful mammalian cloning is very low and not all somatic cell nuclei are capable of producing adult clones. This historical achievement provides a valuable model system in which to address key questions regarding the regulatory mechanisms of genome programming and reprogramming. In addition, it opens wide the debate over ethical issues surrounding the application of this technology, notably in ‘reproductive cloning.’ Nonetheless, the benefits of cloning technology are great, for example as applied to cell and tissue therapy – ‘therapeutic cloning,’ as well as the preservation and propagation of endangered species. Mammalian cloning is an example of how uniparental inheritance has moved from nature into the laboratory with profound implications for genetics and biomedicine.

Uniparental Inheritance

Uniparental inheritance may be achieved passively by simple dilution of mitochondrial genomes in organisms where the sizes of the two gametes are unequal, or by active processes that exclude or eliminate the contribution from one parent. Examples of active processes include exclusion of organelles from gametes or zygotes, degradation of organelles in the gamete or zygote, and exclusion of organelles from embryonic tissue. The largest variety of active mechanisms is found in plants, where uniparental inheritance of the chloroplast genome (sometimes from a different parent) is also the rule. In mammals, sperm mitochondria, which contain ∼100 copies of mitochondrial DNA, enter the zygote, but they are actively eliminated with the sperm remnants during early embryogenesis. Male leakage of mtDNA has been observed in interspecific crosses in mice, suggesting that the factors controlling the elimination of paternal mitochondria are species-specific. Male transmission of mtDNA appears to be extremely rare in humans, a single case having been reported. The fact that uniparental inheritance of organellar genomes is so pervasive suggests that there has been strong selection for this trait throughout evolution. Such a system may have evolved to prevent the spread of mitochondrial genomes with a replicative advantage, but without significant coding-gene content (selfish genomes) in a population. Such genomes have been identified in yeast. Uniparental inheritance would confine selfish genomes to the particular lineage in which they arose.

Allophagy

In sexual reproduction, gamete fusion leads to the combination of two nuclear genomes, but the fate of paternal mitochondrial DNA requires explanation. Cumulative evidence indicates that in most animals, including humans, paternal mitochondria usually are eliminated during embryogenesis, a process termed allophagy, which is accomplished through autophagy.

A number of mechanisms have been proposed to explain allophagy. Some years ago Gyllenstein et al. (1991) hypothesized that according to the “simple dilution model”, the paternal mitochondrial DNA (present at a much lower copy number) is simply diluted away by the excess of oocyte mitochondrial DNA, and consequently the former is hardly detectable in the offspring. On the other hand, according to the “active degradative process”, the paternal mitochondrial DNA or mitochondria themselves are selectively eliminated (either before or after fertilization) by autophagy, preventing their transmission to the next generation (Al Rawi et al., 2012).

As indicated above, uniparental inheritance of mitochondrial DNA is observed in many sexually reproducing species, and may be accomplished by different strategies in different species. Sato and Sato (2012, 2013) have proposed the following strategies.

Diminished content of mitochondrial DNA during spermatogenesis.

Elimination of mitochondrial DNA from mature sperms.

Prevention of sperm mitochondria from entering the oocyte.

Active degradation of the paternal mitochondrial DNA in the zygote.

Selective degradation of the whole paternal mitochondria (mitophagy) in the zygote.

The most feasible mechanism to accomplish this goal in mammals is as follows. Sperm-derived mitochondria and their DNA enter the oocyte cytoplasm during fertilization and temporarily coexist in the zygote alongside maternal mitochondria. However, very shortly after fertilization, paternal mitochondria are eliminated from the embryo. Thus, mitochondrial DNA is inherited solely from the oocyte from which mammals develop. This also means that some human mitochondrial diseases are caused by maternal mitochondrial DNA mutations.

The embryo of the Caenorhabditis elegans nematode has been extensively used as an experimental model for exploring the role of autophagy in the degradation of paternal organelles (Al Rawi et al., 2012). It has been shown that paternal mitochondrial degradation depends on the formation of autophagosomes a few minutes after fertilization. This macroautophagic process is preceded by an active ubiquitination of some spermatozoon-inherited organelles, including mitochondria. The signal for such degradation is polyubiquitination of paternal mitochondria. Sato and Sato (2012) have also reported selective allophagy in such embryos.

It should be noted that the elimination of paternal mitochondrial DNA is not universal. Paternal inheritance of mitochondrial DNA, for example, has been reported in sheep and lower primates (St. John and Schatten, 2004; Zhao et al., 2004). A recent study using mice carrying human mitochondrial DNA indicated that this DNA was transmitted by males to the progeny in four successive generations, confirming the paternal transmission of mitochondrial DNA (Kidgotko et al., 2013). Apparently, human mitochondrial DNA safely passed via the male reproductive tract of several mice in several generations. This and a few other studies invoke a question regarding the existence of a specific mechanism responsible for paternal mitochondrial DNA transmission. Another pertinent, more important, unanswered question is: why are paternal mitochondria and/or their DNA eliminated from embryos? One hypothesis is that paternal mitochondria are heavily damaged by ROS prior to fertilization, and need to be removed to prevent potentially deleterious effects in the next generation (Sato and Sato, 2013).

Evolution of Organelle Uniparental Inheritance

SMI is a case of uniparental inheritance, a common rule for organelle transmission. But why are organelles usually transmitted uniparentally? What are the evolutionary advantages of this non-Mendelian inheritance? Uniparental inheritance may have evolved because it keeps deleterious mutations of organelle DNA within the lineage where they arise, while biparental inheritance would let mutations to spread. In that way a lethal mutation will only lead to extinction of the cell line that contains the mutant organelle, preserving the population. An alternative hypothesis is based upon intragenomic conflicts, which arose with the evolution of cytoplasm-fusing gametes, because this fusion entails a competition between cytoplasmic genes from one gamete and those from the other one. Following this theory, the asymmetry between sexes, and therefore the uniparental inheritance, derives from an asymmetry between nuclear genomes evolved to avoid cytoplasmic gene conflicts through the prevention of biparental cytoplasmic genes transmission. Given that, the intragenomic conflicts might have led to the evolution of separate sexes (ie, only one sex transmitting cytoplasm and organelles). In his review on uniparental inheritance mechanisms and evolution, Birky wrote that “the forces acting on the evolutionary history of uniparental inheritance may be as diverse as those acting on sexual reproduction and as difficult to unravel.” He states that no single hypothesis is sufficient to explain the diverse patterns of uniparental inheritance and suggests a combination of four aspects that could have led to it: (1) chance events (mutation, drift, and extinction), (2) changes in selection coefficients due to presence or absence of cytoplasmic parasites, (3) selection on other features (eg, oogamy), and (4) nucleo-cytoplasmic conflict.

Inheritance Mode

Chloroplasts are generally inherited from only one parent (uniparental inheritance) in seed plants. Maternal inheritance (via the seed parent) is observed as the general pattern in angiosperms. Rare cases of a transmission of cpDNA from the pollen parent to its offspring have been reported. The observation of cpDNA haplotypes after controlled pollination proved maternal inheritance in most instances, although both paternal and biparental inheritance has also been observed. However, ‘paternal leakage’ seems to have a strong impact on the evolution of cpDNA for only few angiosperm plant species.

In contrast, paternal inheritance (via the pollen parent) has been reported for gymnosperms as the general rule. Thus, the chloroplast, mitochondrial, and nuclear genomes are paternally, maternally, and biparentally inherited in gymnosperms including conifers offering unique opportunities to study the distribution of genetic information via seed and pollen for these plants.

Abstract

Maternal inheritance is a group of conceptually related phenomena associated with uniparental inheritance of organelle genomes, cytoplasmic elements, symbionts, substances, and factors, as well as parent-of-origin gene expression effects, and maternally controlled genomic imprinting. Some of these inherited elements direct early ontogeny of an embryo, while others require sufficient offspring development to have an effect. To the extent that such inheritance causally influences development of offspring, they become maternal effects. Despite general conceptual similarity, the types of maternal inheritance have widely distinct mechanisms and evolutionary and genetic consequences.

Inheritance and Usage

In organisms that reproduce sexually, mtDNA is typically inherited from only one of the parental types, that is, uniparental inheritance. Typically, as is the case in most animals, mtDNA is inherited from the maternal parental; hence, we speak of ‘maternal inheritance’. In animals, mtDNA undergoes mutational change more rapidly than single-copy nuclear DNA, and so has been useful in investigating evolutionary relationships through sequence comparisons (phylogenetic analysis). mtDNA has also proven to be of value in genealogical research because offspring, both male and female, inherit it through the maternal line. Analysis of human mtDNA has been employed in forensic laboratories to help identify human remains and in combination with other evidence to implicate or exclude suspects in criminal investigations. Finally, mtDNA has proven to be an invaluable tool in anthropological research and, in recent studies, has even allowed the identification of previously unknown hominid lineages.

9.3.8.2 Maternal transmission

mtDNA is not always maternally transmitted. Zouros (2013) and Breton et al. (2007) reported doubly uniparental inheritance (DUI), a case of paternal transmission in several species of molluscan bivalves. In this method of inheritance, females will transmit their mtDNA to both male and female offspring, and males will transmit their mtDNA only to male offspring resulting in co-occurrence in the same species of two independently evolving mtDNA lineages, one that is transmitted through the eggs and another through the sperm. As a result, females are homoplasmic for the maternal mtDNA but might contain low amounts of paternal mtDNA, and produce eggs with only the maternal mtDNA. However, males are heteroplasmic for both the maternal and the paternal mtDNA but produce sperm that contains only the paternal mtDNA.

Sato and Sato (2013) stated that the mechanisms which confirm the maternal transmission of mtDNA differ in each organism. In mammals, sperm mitochondria are ubiquitinated and subsequently destroyed (Sutovsky et al., 1999); in Drosophila, mitochondria are destroyed during spermatid formation (DeLuca and O'Farrell, 2012); in Oryzias latipes, the mitochondria of the sperm are actively destroyed (Nishimura et al., 2006), and in Caenorhabditis elegans the sperm's mitochondria are destroyed through autophagy (Sato and Sato, 2011; Al Rawi et al., 2011). Maternal inheritance of mtDNA results in homoplasmic individuals, i.e., individuals having a single type of mtDNA. Mishra and Chan (2014) opined that homoplasmy is reinforced by pre- and postfertilization bottlenecks. The prefertilization bottleneck occurs during oogenesis, where the number of mitochondria is critically reduced in the germline, before the maturation of the oocyte. The postfertilization bottleneck occurs between the zygote formation and the blastocyst embryonic stages, during which there is intense cell division but suppression of mitochondrial proliferation, a mechanism that leads to a reduced number of mitochondria per cell.

B. The fate of chloroplast DNA in zygotes

In contrast to the situation in many higher plants, where chloroplasts themselves appear to be transmitted only through the maternal parent (reviewed by Sears, 1980c), gametes of Chlamydomonas fuse in their entirety. For uniparental inheritance to occur under these circumstances, the organelle genome of one parent must be destroyed or at least prevented from replicating. The presumption that uniparentally inherited genes were in fact located in chloroplast DNA prompted Chiang (1968) and Sager and Lane (1972) to investigate the fate of this DNA in young zygotes after mating. Chiang's preliminary conclusion that chloroplast DNA from the minus parent persists after mating was subsequently revised on the grounds that the labeled precursors used to mark DNA from the two parents appeared in a compartmentalized chloroplast DNA pool during zygotic development and were probably recycled into new molecules (Chiang, 1971). Sager and Lane reported, based on data from reciprocal crosses with 14N and 15N-labeled gametes, that chloroplast DNA from the plus parent underwent a density shift within the first 6 hours after gamete fusion, while that from the minus parent disappeared.

Ultrastructural studies of the mating reaction demonstrated that the chloroplasts of the plus and minus gametes fuse between 3 hours and 7 hours after mating (Cavalier-Smith 1970). Microscopic investigation using DAPI staining showed that chloroplast nucleoids from the minus parent disappear even before this time, although this does not necessarily indicate that the chloroplast DNA had actually been destroyed. Within the first 40–50 minutes after mating, the chloroplasts of the parental cells appear to be in close apposition, and nucleoids have disappeared from the chloroplast contributed by the minus parent (Kuroiwa et al., 1982; Coleman, 1984; Figure 7.3). (Kuroiwa established the identity of the gametic chloroplasts within the quadriflagellate zygote by using a mutant with short flagella for one parent in a cross, and by making crosses between small and large gametes. Coleman prestained gametes of one mating type before mating to unstained gametes). Coleman and Maguire (1983) reported that uniparental destruction of chloroplast nucleoids in C. moewusii did not occur until 9–10 hours after mating, at a time when vis-à-vis pairs still persisted and nuclear fusion was just beginning. The decline in visible nucleoids per zygote continued for the next 4–5 hours in zygotes kept in the light but was arrested in zygotes transferred to the dark.

Using optical tweezers and PCR-based analysis on single zygotes formed from transgenic C. reinhardtii gametes expressing the bacterial aadA gene (Chapter 8), Nishimura et al. (1999) demonstrated that chloroplast DNA of the minus parent is actively digested during the period when minus nucleoids disappear, rather than simply diffusing throughout the chloroplast.

Destruction of the minus chloroplast nucleoids is blocked by nuclease-inhibiting agents, such as aurintricarboxylic acid and ethidium bromide, and by cycloheximide, which inhibits protein synthesis on cytosolic ribosomes, but not by inhibitors of chloroplast protein synthesis (Kuroiwa et al., 1983a). In agreement with the studies of Sager and Ramanis (1967), Kuroiwa et al. (1983b, 1985) also found that UV treatment of the plus but not the minus parent interfered with nucleoid destruction. Nishimura et al. (2002) identified a calcium-dependent nuclease activity that was localized to chloroplasts from the minus parent in newly fused cells, but was first detectable in plus gametes during their maturation. This enzyme is active within the first 60–90 minutes after zygote formation, before chloroplast fusion occurs. Nishimura et al. proposed that chloroplast DNA in plus chloroplasts is resistant to digestion, and reviewed the arguments for and against a restriction-modification mechanism, a topic to be discussed more fully in the next section.

After chloroplast fusion, the remaining nucleoids coalesce to a final average of two or three per zygotic plastid (Birky et al., 1984; Coleman, 1984). During germination of the zygote, new chloroplast DNA synthesis appears to occur, as judged by quantitative fluorescence measurements indicating that newly released zoospores contain 3.5 times as much chloroplast DNA as gametes (Coleman, 1984).