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MINIREVIEW / MINISYNTHSE

The inheritance of organelle genes and genomes: patterns and mechanisms1


Jianping Xu

Abstract: Unlike nuclear genes and genomes, the inheritance of organelle genes and genomes does not follow Mendels laws. In this mini-review, I summarize recent research progress on the patterns and mechanisms of the inheritance of organelle genes and genomes. While most sexual eukaryotes show uniparental inheritance of organelle genes and genomes in some progeny at least part of the time, increasing evidence indicates that strictly uniparental inheritance is rare and that organelle inheritance patterns are very diverse and complex. In contrast with the predominance of uniparental inheritance in multicellular organisms, organelle genes in eukaryotic microorganisms, such as protists, algae, and fungi, typically show a greater diversity of inheritance patterns, with sex-determining loci playing significant roles. The diverse patterns of inheritance are matched by the rich variety of potential mechanisms. Indeed, many factors, both deterministic and stochastic, can influence observed patterns of organelle inheritance. Interestingly, in multicellular organisms, progeny from interspecific crosses seem to exhibit more frequent paternal leakage and biparental organelle genome inheritance than those from intraspecific crosses. The recent observation of a sexdetermining gene in the basidiomycete yeast Cryptococcus neoformans, which controls mitochondrial DNA inheritance, has opened up potentially exciting research opportunities for identifying specific molecular genetic pathways that control organelle inheritance, as well as for testing evolutionary hypotheses regarding the prevalence of uniparental inheritance of organelle genes and genomes. Key words: isogamy, anisogamy, paternal leakage, mating type, quantitative organelle inheritance. Rsum : Contrairement aux gnes et gnomes nuclaires, lhrdit des gnes et gnomes des organites ne suit pas les lois de Mendel. Dans cette mini-synthse, lauteur rsumera les progrs rcents en matire des modes et mcanismes dhrdit des gnes et gnomes des organites. Bien que la majorit des eucaryotes sexus montrent une transmission uniparentale des gnes et gnomes des organites chez certaines prognitures au moins une partie du temps, des vidences saccumulent indiquant quune transmission strictement uniparentale est rare et que les modes de transmission sont trs varis et complexes. Au contraire de la prdominance de la transmission uniparentale chez les organismes multicellulaires, les gnes des organites chez les microorganismes eucaryotes, tels que les protistes, algues et champignons, montrent typiquement une plus grande diversit de modes de transmission et les locus dterminant le sexe jouent un rle significatif dans ces phnomnes. Aux divers modes de transmission sajoutent une grande varit de mcanismes potentiels. En effet, plusieurs facteurs tant dterministes que stochastiques peuvent influencer le mode de transmission des organites. Chez les organismes multicellulaires, les prognitures issues de croisements interspcifiques semblent montrer plus souvent des fuites paternelles et une transmission biparentale que celles provenant de croisements intraspcifiques. La dcouverte rcente dun gne dterminant le sexe chez le Cryptococcus neoformans qui contrle la transmission de lADN mitochondrial offre de nouvelles opportunits excitantes pour identifier des sentiers molculaires spcifiques qui contrleraient la transmission des organites et pour tester des hypothses volutives concernant la prdominance de lhrdit uniparentale. Mots cls : isogamie, anisogamie, fuite paternelle, type sexuel, hrdit quantitative des organites. [Traduit par la Rdaction] Xu 958

Received 3 May 2005. Accepted 24 August 2005. Published on the NRC Research Press Web site at http://genome.nrc.ca on 29 November 2005. Corresponding Editor: R.S. Singh. J. Xu. Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; and Institute of Tropical Medicine, Hainan Medical College, Haikuo, Hainan, China (e-mail: jpxu@mcmaster.ca).
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This article is based on a talk presented as the recipient of the Robert Haynes Young Scientist Award at the 2005 Annual Meeting of the Genetics Society of Canada held at Banff, Alberta.
doi: 10.1139/G05-082 2005 NRC Canada

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Introduction
One of the major differences between prokaryotic and eukaryotic cells is that eukaryotic cells contain a diverse array of subcellular organelles. Among these organelles, the chloroplasts (in plants and algae) and mitochondria (in almost all eukaryotes) are distinctive in that they contain their own genetic material. These two organelles play vital roles in eukaryotic bioenergetics: chloroplasts, by converting sunlight energy to chemical energy, and mitochondria, by converting chemical energy to ATP through oxidative phosphorylation. Because of their important biological functions, deleterious mutations affecting mitochondria and chloroplasts can have profound effects. For example, human mutations affecting mitochondrial functions can have devastating consequences for the host (Naviaux and McGowan 2000). As a result, there have been significant research efforts to understand the structure, function, and inheritance of mitochondria and chloroplasts. The focus of this mini-review is on the inheritance of organelle genes and genomes. Organelle genes and genomes have patterns of inheritance distinctively different from those of nuclear genes and genomes. The different patterns were first noticed about a century ago, soon after the rediscovery in 1900 of Mendels laws of nuclear inheritance. Baur (1909) and Correns (1909) independently observed the nonMendelian patterns of inheritance of the green-white variegation in 2 plant species, Pelargonium and Mirabilis. Such variegation patterns were later found in many plants, largely as a result of mutations in chloroplast genomes (e.g., Kuroiwa et al. 1993; for a summary see Gillham 1994). In 1933, Rhoades made the first observation of nonMendelian inheritance of a mitochondrial mutation that caused cytoplasmic male sterility in corn. However, it was not until the 1960s that chloroplasts and mitochondria were convincingly shown to have their own genomes and contain their own replication, transcription, and translation machinery. The study of organelle genes and genomes has since flourished. Over the years, scientists have identified several features that distinguish organelle and nuclear genes and genomes (for a review, see Gillham 1994). First, during the evolution of eukaryotic cells, there has been a unidirectional transfer of genetic information from the organelles to the nuclear genome. The net result is that the nuclear genome contains vastly more information than its organelle counterparts. Second, through the endosymbiotic evolutionary process, organelle genomes have lost their ability to independently replicate, transcribe, and translate without the help of proteins and other biomolecules encoded by the nuclear genome. In contrast, each nuclear genome typically contains all the genetic information for its own replication, transcription, and translation. Third, nuclear genomes are stringent genomes, whereas organelle genomes are relaxed genomes. During each mitotic cell cycle, each nuclear genome is replicated exactly once, and each daughter cell receives only one set of genes. In contrast, organelle genomes within a cell typically replicate randomly and partition into daughter cells randomly during cell division (Birky 1994). Fourth, nuclear genomes segregate predominantly during sexual reproduction and very rarely during somatic growth. In contrast, organelle genomes often segregate during mitotic division and somatic growth. Fifth, each eukaryotic cell typically has multiple organelles,

and each organelle may have multiple genomes. As a result, there may be extensive intracellular and intercellular competition and selection among organelle genomes within cells (Birky 1973). And lastly, during sexual reproduction, nuclear genes and genomes follow Mendelian laws, while organelle genes and genomes do not obey these laws. In this mini-review, I briefly summarize our current understanding of the patterns and mechanisms of organelle gene and genome inheritance in sexual crosses. While the predominant pattern of organelle DNA inheritance is uniparental and maternal, there is increasing evidence indicating that this view is overly simplistic. Furthermore, molecular, cellular, and microscopic analyses suggest that potential mechanisms for uniparental organelle inheritance are highly variable. Patterns of organelle inheritance during sexual mating Decades of research from plants, animals, protists, and fungi have demonstrated that while uniparental inheritance predominates, there is a wide variety of inheritance patterns for organelle genes and genomes. In this section, I will briefly describe the patterns of organelle inheritance in the different groups of eukaryotes, highlighting exceptions to the rule of uniparental inheritance. Animals Mitochondria are ubiquitous in animal cells. In intraspecific crosses examined so far, almost all animal species show that mitochondrial DNA (mtDNA) is inherited exclusively from the maternal parent. However, 2 exceptions have been noted. The first is the mussel (Zouros 2000). Species of the families Mytilidae (sea mussel) and Unionidae (fresh water mussel) contain 2 types of mtDNA, the F type and the M type. The F type mtDNA behaves like standard animal mtDNA, while the M type is transmitted through the sperm and establishes itself only in the male gonads. Therefore, these 2 mtDNA types have separate transmission routes one through the female lineage, and the other through the male lineage. This phenomenon has been called doubly uniparental inheritance (DUI). The second exception was reported in a 28-year old human male patient with mitochondrial myopathy. The mtDNA in the muscle tissue of this patient was from his father, while that in his blood was from his mother (Schwartz and Vissing 2002). In interspecific crosses in animals, the pattern of mitochondrial inheritance is more variable but largely consistent with the observations in intraspecific crosses. For example, in 1 experiment, Lansman et al. (1983) performed a critical test of the exclusivity of maternal mitochondrial inheritance in animals. They constructed repeated backcrosses between the tobacco budworm Heliothis virescens and its close relative Heliothis subflexa. The rationale for their repeated backcrosses was that previous data suggested that maternal inheritance of animal mtDNA in both intra- and inter-specific crosses had almost exclusively come from single-generation mating experiments, and because of large differences between male and female gametes in cytoplasmic contents (including organelles), the existence of minute amounts of paternal mtDNA could have escaped detection. To eliminate the effects derived from methodological deficiencies, they constructed long-term mating experiments in which a fertile
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female lineage derived from the hybridization of the 2 moth species was backcrossed repeatedly to the male parental species. The objective was to increase the likelihood of possible low-level paternal leakage. Progeny from backcrosses between the 45th and 91st generations were analyzed using autoradiographic techniques that could detect rare mtDNA molecules that were present in numbers fewer than 1 per 500 molecules. Their analysis failed to detect any paternal mtDNA and set an upper limit of paternal leakage at about 1 molecule per 25,000 per generation in this system (Lansman et al. 1983). Using similar techniques and strategies, Gyllensten et al. (1985) showed that interspecific backcrosses through 68 generations in both directions between 2 species of mouse, Mus domesticus and Mus spretus, failed to show any evidence of paternal leakage. However, in a subsequent analysis of the same crosses using the more sensitive technology of PCR, they detected paternal mtDNA leakage (Gyllensten et al. 1991). They estimated that the number of paternal mtDNA molecules that can enter the egg cytoplasm and persist was 14 per 100,000 maternal mtDNA molecules per generation. However, the first reported paternal mtDNA leakage in an animal species was found by Kondo et al. (1990) in their analysis of an interspecific cross between Drosophila simulans and Drosophila mauritiana. More recently, paternal mtDNA leakage was detected in a natural hybrid zone between 2 subspecies of the great tit (Parus major) in the middle Amur Valley in eastern Siberia (Kvist et al. 2003). As shown above, though maternal inheritance is the major mode of mtDNA transmission in animals, there is increasing evidence from both natural population surveys and experimental crosses that paternal leakage and biparental inheritance may be more common than previously thought. The examples presented above include several major groups of animals, including insects (Drosophila), mollusks (Mytilus), birds (Parus), and mammals (mouse and human). It is likely that similar paternal mtDNA leakage could occur in other groups of animals. Plants All plants have 2 distinct types of organelles that contain their own genetic materials: chloroplasts and mitochondria. The transmission of mtDNA and chloroplast DNA (cpDNA) has been investigated in many plant species. For example, organelle inheritance was recently investigated in a representative of the earliest land plants, the liverwort Pellia. Pacak et al. (2003) demonstrated that all individuals from 14 populations of a natural hybrid liverwort species, Pellia borealis, contained both chloroplast and mitochondrial genomes from only 1 of the 2 parents, Pellia epiphylla species N, with none from the other parent, P. epiphylla species S. This result is consistent with an ancient origin of uniparental organelle inheritance in plants. However, the 2 large groups of vascular plants, angiosperms and gymnosperms, show markedly different patterns of organelle inheritance. In angiosperms, cpDNA transmission is often maternal. However, biparental transmission has been observed in at least 20 genera, including the common garden flower Petunia hybrida, potato (Solanum tuberosum), geranium (Pelargonium zonale), and the evening primrose (Oenothera

spp.) (Gillham 1994). In contrast with angiosperms, the transmission of cpDNA in gymnosperms (e.g., pine, fir, spruce, and redwood) is predominantly paternal (Neale and Sederoff 1988). In interspecific crosses, the incidence of biparental inheritance is also high. For example, among 6 hybrids generated from a cross between 2 larch (Larix) species, 3 showed strict paternal cpDNA inheritance, 1 contained maternal cpDNA, and 2 contained cpDNA from both parents (Szmidt et al. 1987). More recently, interspecific hybrids between 2 angiosperms, rye and wheat, showed extensive paternal cpDNA leakage and biparental cpDNA inheritance (Siniavskaia et al. 2004). In angiosperms, the pattern of mtDNA inheritance is similar to the transmission of cpDNA: i.e., it is predominantly maternal with low but frequent paternal leakage and biparental mtDNA inheritance. Interestingly, in all gymnosperms examined (except the redwood), mtDNA is transmitted predominantly from the maternal parent (the ovum), in contrast with the predominantly paternal inheritance of cpDNA (Neale et al. 1989). Unicellular eukaryotes The inheritance of organelle DNA has been examined in many unicellular eukaryotes, including several model species, such as the budding yeast Saccharomyces cerevisiae and the green alga Chlamydomonas reinhardtii. Diverse patterns of organelle inheritance have been reported among this group of organisms. In both Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe, mtDNA inheritance is biparental and the initial zygotes are heteroplasmic. This is expected, because zygotes in these yeasts are the products of simple fusions between cells with different mating types. Biparental mtDNA inheritance has also been observed in the human pathogenic protist Trypanosoma brucei, which causes African sleeping sickness (Gibson 2001). In other unicellular eukaryotes, the zygotes are formed in a way that is similar to that of the budding and fission yeasts, but the organelle genomes examined so far show a largely mating-type dependent uniparental inheritance. Some well known examples include Chlamydomonas reinhardtii, the slime mold Physarum polycephalum, and the basidiomycete yeast Cryptococcus neoformans. The following is a brief summary of these patterns. There are 2 mating types in the human pathogen Cryptococcus neoformans, MATa and MAT. In sexual crosses between MATa and MAT strains, progeny typically inherit mtDNA from the MATa parent (Xu et al. 2000; Yan and Xu 2003), though low-level leakage is not uncommon. Results from the analysis of natural hybrids have been consistent with laboratory crosses (Xu 2002; Xu et al. 2002; Yan and Xu 2003). Unlike Cryptococcus neoformans, which has only 2 mating types, there are at least 13 functionally different alleles at the sex-determining matA locus in Physarum polycephalum. mtDNA in this protist is inherited largely uniparentally, according to the relative sexuality determined by the mating type alleles. In fact, the 13 matA alleles can be ranked in a linear hierarchy of dominance. The mtDNA donor is typically the strain that possesses the dominant matA allele in the linear hierarchy (Moriyama and Kawano 2003). A simi 2005 NRC Canada

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lar mating-type-dependent uniparental mtDNA inheritance is observed in another slime mold, Polysphondylium pallidum. Polysphondylium pallidum has 2 mating types, mat1 and mat2. Progeny from crosses between mat1 and mat2 strains typically inherit mtDNA from the mat2 parent (Mirfakhrai et al. 1990). In the green alga Chlamydomonas reinhardtii, mtDNA is inherited from the mating type minus (mt) parent. However, cpDNA shows the opposite pattern, since it is inherited almost exclusively from the mating type plus (mt+) parent (Gillham 1994). When sample sizes are large, leakage of mtDNA, cpDNA (in Chlamydomonas reinhardtii), biparental inheritance, and recombinant organelle genotypes have been detected in all of the unicellular eukaryotes mentioned above. Filamentous fungi Mitochondrial inheritance in filamentous fungi is somewhat different from that in plants, animals, and unicellular eukaryotic microbes. Fungi contain 4 major divisions: Basidiomycota, Ascomycota, Zygomycota, and Chytridiomycota. In interspecific crosses of the aquatic Chytridiomycete (Allomyces spp.), mtDNA is inherited paternally (Borkhardt and Olson 1983). In all sexual filamentous ascomycetes, there are 2 mating types, and mating between strains can occur via 2 different processes. In the first process, 2 morphologically differentiated gametes/cells with different mating types mate. In these crosses, mtDNA is typically inherited from the larger, maternal gamete, the protoperithecia. Both mating types can act as the maternal or paternal parent. In the second mating process, vegetatively compatible mycelia fuse, and progeny from such fusion events often show biparental mitochondrial inheritance, although uniparental inheritance is not uncommon. Species in the genera Neurospora, Aspergillus, and Podospora have been examined extensively for patterns of mtDNA inheritance (Yan and Xu 2005). Unlike filamentous ascomycetes, typical filamentous basidiomycetes mate only via mycelial fusion between the morphologically undifferentiated mycelia or yeasts of 2 compatible homokaryotic or monokaryotic cultures. A number of filamentous basidiomycete species have been examined for mtDNA inheritance in laboratory matings, including Agaricus bisporus (de la Bastide and Horgen 2003) and Armillaria bulbosa (Smith et al. 1990). In a typical mating, nuclei from the 2 parents migrate and replicate through their partners cytoplasm after mycelial fusion, while mitochondria do not migrate. As a result, the final mating product has a homogeneous nuclear genotype with each cell containing the nuclear genomes from both parents. In contrast, while mitochondrial genomes from both parents persist in the mating colony, most cells have only 1 mtDNA genotype. However, variations exist among the species and strains in terms of nuclear migration and cytoplasmic mixing. For example, in the button mushroom Agaricus bisporus, nuclear migration is very limited during mating (Xu et al. 1993). As a result, the heterozygous mating products are restricted only to the zone of mycelial fusion where cytoplasmic mixing occurs. Indeed, both biparental inheritance and recombinant mitochondrial genotypes can be found in heterokaryons in this junction zone (e.g., de la Bastide and Horgen 2003). Similarly, in another mushroom species, Agrocybe aegerita, uniparental, biparental, and recombinant mtDNA genotypes

were observed among zygotes (Barroso and Labarere 1997). Most of the studies of filamentous fungi used laboratory crosses. Analyses of natural populations may show slightly different patterns. For example, in the root-rot fungus Armillaria bulbosa, all natural clones (defined as having the same nuclear genotype at multiple loci) were found to have only 1 mitochondrial genotype each, unlike laboratory observations that mating products are mosaics of mitochondrial genomes (Smith et al. 1990). It should be noted that in all laboratory investigations of filamentous fungi, it was always possible, in a given pairing, to recover both types of mtDNA among sexual progenies. Mechanisms of organelle DNA inheritance in sexual mating Currently, the molecular, genetic, and cellular pathways responsible for organelle inheritance have not been investigated in most species. However, it is generally agreed that no single mechanism will be able to explain all of the inheritance patterns observed so far. Since sexual reproduction is the stage in an organisms life cycle that most likely influences organelle inheritance, the potential underlying mechanisms can be roughly divided into 3 categories: prefertilization, fertilization, and postfertilization. Prefertilization mechanisms Prefertilization mechanisms are those involved in gametogenesis, prior to the fusion of gametes. One of the most common prefertilization mechanisms involves differences in gametic size and the associated differences in organelle population size in these gametes. In most unicellular eukaryotic microbes, mating partners have similar sizes and are typically morphologically indistinguishable (isogamy). These isogamous gametes contain similar numbers of organelles and organelle genomes. As a result, prefertilization mechanisms should not apply here. However, in the isogamous species of the green algal genus Temnogyra, there is evidence for active degradation of chloroplasts in 1 type of gamete during gametogenesis (Birky 1995). Unlike isogamous unicellular eukaryotic microbes, most plants and animals are anisogamous. During gametogenesis, because of unequal cell division or differential growth, or both, morphologically distinct sexual gametes are produced, with the maternal gametes being much larger than the paternal gametes. In mice and humans, the number of organelle genomes in the sperm is estimated in the hundreds, while that in the egg is around 1 000 000 (Gillham 1994). A natural consequence of this is that the input of organelle genomes in the zygote is biased in favour of the maternal organelles. Even if paternal organelle genomes enter the egg, they are difficult to detect without using extremely sensitive techniques to screen a large population of progeny. While the biased input ratio of organelle DNA in favour of maternal organelles may explain the majority of uniparental organelle inheritance in plants and animals, in some species, such as the crayfish, mitochondrial genomes are completely excluded from the sperm by unequal cytokinesis during gametogenesis (Moses 1961). Similarly, in the anisogamous green alga Bryopsis, both cpDNA and mtDNA are destroyed during the differentiation of male gametes (Kuroiwa and Uchida 1996).
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Fertilization mechanisms Fertilization mechanisms refer to the processes operating during mating. In isogamous unicellular eukaryotes, zygotes are typically formed by the fusion of genetically compatible gametes or somatic cells. Thus, in unicellular eukaryotes, each zygote should contain the complete cytoplasms (and the 2 sets of nuclei) from both parental gametes. Consequently, we expect the organelle genomes from both parents to be present in the zygote. Most species seem to confirm this null hypothesis. The only exception directly observed so far is the ciliated protist Paramecium. In this species, cells from the 2 mating partners do not completely fuse. Instead, nuclei from the 2 mating partners exchange genetic material during fertilization, while organelles remain separate and do not mix or exchange genetic material (Gillham 1978). The other exception may be in the fungus Cryptococcus neoformans. In this species, preliminary data suggest that mitochondria and mtDNA from the MAT parent may be excluded from entering the zygote (Yan and Xu 2003; Yan et al. 2004). Microscopic observations suggest that mating in Cryptococcus neoformans involves conjugation tube formation by the MAT parent and the enlargement of the MATa cell just prior to cell fusion (McClelland et al. 2004). It is therefore possible that during zygote formation, the MAT nucleus migrates through the conjugation tube into the MATa cell, while mitochondria from the MAT parent are left behind. In contrast, the exclusion of organelles and organelle genomes predominates during fertilization in the majority of filamentous basidiomycete fungi (see above; Yan and Xu 2005). This exclusion may be considered a byproduct of reciprocal nuclear migration, not an active process specifically targeting the organelle genes and genomes. In the majority of anisogamous species, such as plants and animals, fertilization mechanisms may play a role, but direct evidence for or against the active exclusion of organelle and organelle genomes is very limited. In 1 species, the tunicate Ascidia, there is evidence for loss of mitochondria in the sperm just prior to entry into the egg (Ursprung and Schabtach 1965). Postfertilization mechanisms Postfertilization mechanisms refer to the processes operating after the formation of the zygote. Several postfertilization mechanisms have been documented. In the green alga Chlamydomonas reinhardtii and the slime mold Physarum polycepharum, differential staining and fluorescent microscopy identified the active degradation of organelle DNA by nucleases (Moriyama and Kawano 2003; Nishimura et al. 2002). However, in both cases, the nature of the nucleases and their relationships to mating-type loci (mating-type loci here are the genetic determinants of organelle inheritance in both species, see also above) are unknown. Processes during the development of zygotes and embryos can also influence organelle inheritance. For example, during the development of fertilized eggs of the gymnosperm Larix, the future embryonic cytoplasm is partitioned into a special region of the zygote that includes only paternal chloroplasts and maternal mitochondria, while maternal chloroplasts and paternal mitochondria are excluded from this cytoplasmic region (Szmidt et al. 1987).

One of the most extensively studied species for organelle genetics is the budding yeast Saccharomyces cerevisiae. In this species, all initial zygotes contain organelle genomes from both mating partners. However, during subsequent budding, while the nuclear genomes remain diploid, organelle genomes segregate rapidly among the buds (Birky 1994). The position of the new buds is a highly reliable predictor of organelle genotypes in the new bud. Specifically, buds from the middle of the zygote, where 2 gametes have fused, are more likely to contain mitochondrial genomes from both parents, while buds from the 2 ends are dominated by the organelle genome of 1 parent or the other. This is because the mixing of mitochondrial genomes in zygotes is very limited in Saccharomyces cerevisiae. In contrast, mitochondrial proteins mix rapidly (Berger and Yaffe 2000). Extensive research efforts are underway to determine the molecular mechanisms controlling the differential mixing of mitochondrial DNA and protein movements in the budding yeast. Nongenetic factors The above sections summarize mostly genetic mechanisms that influence the inheritance of organelle genes and genomes. As alluded earlier, several nongenetic factors can also influence our observations of organelle inheritance. For example, in the button mushroom Agaricus bisporus, mating condition (age of culture, medium, and size of inoculum) can have a significant influence on mitochondrial inheritance (e.g., de la Bastide and Horgen 2003; Yan and Xu 2005). In addition, sample size, sampling procedures, and the techniques we use to determine organelle genotype, can all have significant influences on our observations. For example, in the budding yeast, the position of a bud has a major effect on bud organelle genotype. Similarly, in filamentous basidiomycetes, sampling location often has a predictable effect on zygote organelle genotype. Genetic determinants Despite extensive research efforts in the last 40 years since the discovery that organelles contain their own genes and genomes, in only very few cases do we know anything about the genes or molecular pathways that influence the inheritance of organelle genes and genomes. One of the most intensively studied species is the unicellular alga Chlamydomonas reinhardtii. Boynton et al. (1987) first reported, almost 20 years ago, that both the chloroplast genome and the mitochondrial genome were inherited predominantly uniparentally, though from different parents. Since then, a variety of models have been proposed (e.g., Gillham 1994; Nishimura et al. 2002). Genetic analyses have demonstrated that the mating type locus controls organelle inheritance, with the mt parent contributing mtDNA and the mt+ parent transmits cpDNA (Gillham 1994). Furthermore, it was recently found that an mt+ gamete-specific nuclease specifically targets the mt chloroplasts during sexual reproduction in Chlamydomonas reinhardtii (Nishimura et al. 2002). However, the location of this nuclease gene and its relationship to the mating type locus have not been identified. Our understanding of the uniparental mtDNA inheritance in the slime mold Physarum polycepharum is at a level similar to that for Chlamydomonas reinhardtii. In a recent study, Moriyama and Kawano (2003) showed that
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rapid, selective digestion of mtDNA occurs in this species and that the digestion follows the same hierarchy as the matA hierarchy of the multiallelic mating types in this species. Currently, nothing is known about the relationship between the mating type locus and the nuclease gene in this slime mold. In the basidiomycete yeast Cryptococcus neoformans, we also identified that the mating type locus controls mitochondrial inheritance (Yan and Xu 2003). Furthermore, we identified, within the ~100 kb region of the MAT locus, a sexspecific gene, sxi1, that controls mitochondrial inheritance (Yan et al. 2004). Disruption of the MAT-specific gene resulted in biparental mtDNA inheritance, significant heteroplasmy (zygotes with organelle genomes from both parents), and recombinant mitochondrial genomes. Interestingly, the SXI1 protein has a structure and function similar to other sex-determining genes such as the SRY gene in mammals (Haqq and Donahoe 1998) and the gamete-specific gene GSP1 in Chlamydomonas reinhardtii (Kurvari et al. 1998). SRY is male specific, located on mammalian Y chromosomes. In contrast, GSP1 is present in both mt+ and mt mating types but is expressed only in the mt+ gamete. Currently, the potential roles of SRY and GSP1 in mitochondrial inheritance in mammals and algae have not been examined. However, it is worth noting that in these evolutionarily divergent systems, parental gametes carrying these homeodomain genes function as males and contribute only nuclei but not mitochondria to their progeny. Microscopic observations suggest that during mammalian fertilization, the entire midpiece of the sperm degenerates within the mammalian egg (e.g., Sutovsky et al. 2000). Sutovsky et al. (1999, 2000) provided evidence that during spermatogenesis in cows and rhesus monkeys, ubiquitin is bound to the sperm mitochondria. The injection of antiubiquitin antibodies into a fertilized egg prevents the degradation of the sperm mitochondria. Because ubiquitin binds to proteins and marks them for degradation by proteasomes and lysosomes, Sutovsky et al. (2000) suggested that ubiquitination is involved in the active degradation of sperm mitochondria. Evolutionary considerations and perspectives Over the past several decades, there has been much speculation as to why uniparental organelle inheritance is so prevalent among eukaryotes. Phylogenetic evidence indicates that the pattern of uniparental organelle inheritance has likely evolved multiple times in the eukaryotic domain (Birky 1995). In evolutionary terms, uniparental inheritance effectively results in asexual genomes. Both theoretical and experimental investigations have shown that asexual genomes are highly susceptible to mutational pressure (e.g., Xu 2004a, 2004b). The largely asexual nature of organelle genomes forms a sharp contrast with the recombining nature of nuclear genomes in sexual eukaryotes. There are several hypotheses for the difference. One hypothesis suggests that maternally and paternally derived organelles directly compete against each other in the zygote cytoplasm, creating an intracytoplasmic conflict (Cosmides and Tooby 1981). Because such a conflict could be costly for the zygotes, a nuclear gene that can suppress its associated organelles and prevent them from being transmitted would

have an evolutionary advantage and spread through the population. The second hypothesis suggests that uniparental organelle inheritance evolved to limit the spread of deleterious mutations in organelle genes and genomes. In mammals, the per nucleotide mutation rate in mitochondrial genes is about 10 20 times higher than that of nuclear genes (Jansen 2000). Some of the mutated mitochondrial genomes may have replication advantages but exert deleterious effects on cell function and organismal performance. Uniparental inheritance could limit the spread of such mutants. The third hypothesis is that uniparental organelle inheritance is a byproduct of other evolutionary processes, such as mating success (e.g., anisogamy) and nuclear migration (e.g., in filamentous basidiomycetes), but has few evolutionary adaptive consequences of its own. It should be noted that hypotheses I and II are not mutually exclusive. Indeed, all 3 hypotheses may be consistent with uniparental mitochondrial inheritance in the same or different groups of organisms. Currently, experimental evidence for all 3 is ambiguous. However, several observations, described below, are inconsistent with the second hypothesis. Selfish mitochondrial plasmids have been found in many species. In most cases, these plasmids are transmitted in the same manner as the mitochondrial genomes (Gillham 1994). However, in the slime mold Physarum polycephalum, the linear mitochondrial plasmid mF can bypass uniparental mitochondrial inheritance and be transmitted to mF strains, regardless of the mating-type hierarchy of the parental strains (Sakurai et al. 2004). In the filamentous ascomycete Neurospora, the transmission patterns of mitochondrial plasmids Fiji, kalilo, and Hanalei-2 are different from that of their mitochondrial genomes (May and Taylor 1989; Yang and Griffiths 1993). Similar observations have been made for a mitochondrial plasmid in rapeseed, Brassica napus (Handa et al. 2002). Therefore, uniparental organelle inheritance is not a stringent barrier for controlling the spread of selfish cytoplasmic genetic elements. Over the last decade, extensive progress has been made in our understanding of the patterns and mechanisms of organelle gene and genome inheritance. With the advent of more sensitive techniques and analytical tools, organelle genetics is poised to make significant strides. For example, with the discovery that a single transcription factor, SXI1, controls mitochondrial inheritance in Cryptococcus neoformans, downstream targets and molecular mechanisms can be identified using molecular genetic tools. Furthermore, because mitochondrial inheritance can now be controlled in Cryptococcus neoformans, this species may also offer an excellent system for testing the various hypotheses for the evolutionary advantage(s) of uniparental mitochondrial inheritance. More generally, rather than a qualitative dichotomic trait, increasing evidence suggests that organelle inheritance should be treated as a quantitative trait (Birky 2001). The application of quantitative genetic tools will further enrich our understanding of the dynamics of the organelle genome within an organelle, among organelles within a cell, among cells and tissues within an individual, and among individuals within a population.
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Acknowledgements
I thank Dr. Rama Singh, the Review Editor for Genome, and Dr. Peter Moens, the Editor-in-Chief for Genome, for their support and encouragement for this review. I thank Heather Yoell and an anonymous reviewer for comments, and Zhun Yan for his valuable contribution to our ongoing work on mitochondrial inheritance in Cryptococcus neoformans. My research is supported by grants from the Natural Science and Engineering Research Council of Canada, the Premiers Research Excellence Award, Genome Canada, the Canadian Foundation for Innovation, and the Ontario Innovation Trust.

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