EXTRACHROMOSOMAL INHERITANCE

Outside the nucleus, DNA is found in the mitochondrion and the chloroplast. The genes in these mitochondrial and chloroplast genomes are known as extranuclear genes, extrachromosomal genes, cytoplasmic genes, non-Mendelian genes, or organellar genes. These non-Mendelian, extranuclear genes do not follow the rules of

Mendelian inheritance, as do nuclear genes. Cytoplasm is inherited from the mother in many organisms, so the inheritance of extranuclear genes in these organisms is strictly maternal. Extranuclear inheritance differs from maternal effect in two related respects:

(1) The phenotype in extranuclear inheritance is determined by an individual’s organellar gene, whereas the phenotype in maternal effect is determined by a nuclear gene in the mother of the individual; and

(2) An individual’s phenotype in extranuclear inheritance matches its genotype, whereas an individual’s phenotype in maternal effect does not match its own genotype, instead matching that of its mother.

Extranuclear Genomes

1. Mitochondrial DNA (mt DNA) The genomes of mitochondria (known as mtDNA) of many organisms are circular,

double-stranded, supercoiled DNA molecules. Linear mitochondrial genomes are found in some protozoa and some fungi. In general, mitochondrial (mt)DNA contains information for a number of mitochondrial components such as tRNAs, rRNAs, and some of the polypeptide subunits of the proteins cytochrome oxidase, NADH-dehydrogenase, and ATPase. The other components found in the mitochondria—most of the proteins in the organelles— are encoded by nuclear genes and are imported into the mitochondria. These components include the DNA polymerase and other proteins for mtDNA replication, RNA polymerase and other proteins for transcription, ribosomal proteins for ribosome assembly, protein factors for translation, the aminoacyl–tRNA synthetases, and the other polypeptide subunits for cytochrome oxidase, NADH-dehydrogenase, and ATPase. Two general patterns are found in mitochondrial inheritance in animals.

a. First, the mitochondria are generally inherited in a maternal fashion; that is, the male gamete usually does not contribute mitochondria to the zygote. However, a small amount of “leakiness” occurs in this process. For example, it has recently been shown that about one mitochondrion per thousand is of paternal (From father) origin in mice. In some species, such as mussels, it appears that mitochondrial inheritance is biparental. That is, the population of mitochondria in an offspring derives almost

equally from the male and female parent.

In some gymnosperm plants, such as coastal redwoods, mitochondria are inherited paternally—only paternal mitochondria are passed into the zygote. However, these are all exceptions to the general rule of maternal inheritance of mitochondria.

b. The second general pattern of mitochondrial inheritance is omoplasmy, the

existence of a uniform population of mitochondria within an organism. In general, all the mitochondria within an individual are genetically identical. Certainly, biparental inheritance and leakiness of paternal mitochondria violate that principle, resulting in heteroplasmy, a heterogeneity of mitochondria within a cell or organism.

2. Chloroplast DNA (cp DNA)

chloroplast (cp)DNA is double-stranded, circular, and supercoiled. The chloroplast genome contains genes for the rRNAs of chloroplast ribosomes, for tRNAs, and for some of the proteins required for transcription and translation of the cp-encoded genes (such as ribosomal proteins, RNA polymerase subunits, and translation factors) and for photosynthesis. Most of the proteins found in the chloroplast are encoded by nuclear genes.

3. Plasmids 4. Viral Genomes in a cell or symbiotic particles that have their own genetic material

Rules of Extranuclear Inheritance The pattern of inheritance shown by extranuclear genes is known as extranuclear inheritance or non-Mendelian inheritance, and it differs strikingly from the pattern shown by nuclear genes.

Four main characteristics of extranuclear inheritance:

1. Ratios typical of Mendelian segregation are not found, because meiosis-based

Mendelian segregation is not involved.

2. In multicellular eukaryotes, the results of reciprocal crosses involving extranuclear

genes are not the same as reciprocal crosses involving nuclear genes, because

meiosis-based Mendelian segregation is not involved. Mitochondrial and chloroplast

genes usually show uniparental inheritance from generation to generation. In

uniparental inheritance, all progeny (both males and females) have the phenotype of

only one parent. Usually for multicellular eukaryotes, the phenotype of the mother is

inherited exclusively, a phenomenon called maternal inheritance. Maternal inheritance

occurs because the amount of cytoplasm in the female gamete usually greatly exceeds

that in the male gamete. Therefore, the zygote receives most of its cytoplasm

(containing the extranuclear genomes of the mitochondria and, where applicable, of the

chloroplasts) from the female parent and a negligible amount from the male parent.

3. Extranuclear genes cannot be mapped to the chromosomes in the nucleus.

4. Extranuclear inheritance is not affected by substituting a nucleus with a different

genotype.

Maternal effects are the influences of a mother’s genotype on the phenotype of her offspring; examples include snail coiling and moth pigmentation Cytoplasmic inheritance is controlled by nonnuclear genomes found in chloroplasts,

mitochondria, infective agents, and plasmids. And imprinting is a process in which gene expression depends on the parent from which the gene came. None of these modes of inheritance follow the usual Mendelian rules and ratios. Maternal effects result from the asymmetric contribution of the female parent to the development of zygotes. Although both male and female parents contribute equally to the zygote in terms of chromosomal genes (with the exception of sex chromosomes), the sperm rarely contributes anything to development other than chromosomes. The female parent usually contributes the zygote’s initial cytoplasm and organelles. Zygotic development, therefore, usually begins within a maternal milieu, so that the maternal cytoplasm directly affects zygotic development Cytoplasmic inheritance refers to the inheritance pattern of organelles and parasitic or symbiotic particles that have their own genetic material. Chloroplasts, mitochondria, bacteria, viruses, and, of course, plasmids all have their own genetic material. These genomes are open to mutation, their inheritance pattern does not follow Mendel’s rules for chromosomal genes. Imprinting occurs in more than twenty genes and is responsible for several human diseases. Note: Some environmentally induced traits persist for several generations. For example, a particular Drosophila strain that normally grows at 21 degC was exposed to 36degC for twenty-two hours. Dwarf progeny were produced. When they were mated among themselves, fewer and fewer dwarfs appeared in each generation, but smaller than- normal flies were produced as late as the fifth generation. The appearance of an environmentally induced trait that persists for several generations has been termed dauermodification. MATERNAL EFFECTS

Snail Coiling Snails are coiled either to the right (dextrally) or to the left (sinistrally) as determined by holding the snail with the apex up and looking at the opening. The snail is dextrally coiled if the opening comes from the right-hand side and sinistrally coiled if it comes from the left-hand side.

In the left half of figure, a dextral snail provides the eggs, and a sinistral snail provides the sperm. The offspring are all dextral; presumably, therefore, dextral coiling is dominant. When the F1 are self-fertilized (snails are hermaphroditic), all the offspring are dextrally coiled. The result is unexpected. Nevertheless, when the F2 are self-fertilized, one-fourth produce only sinistral offspring, and three-fourths produce only dextral offspring. When the reciprocal cross is made (fig. right), the F1 have the same genotype as just described but are coiled sinistrally, as is the female parent. From here on, the results are exactly the same for both crosses. In both cases, the F1 are phenotypically similar to the female parent even though the offspring in both crosses have the same genotype (Dd). The explanation is that the genotype of the maternal parent determines the phenotype of the offspring, with dextral dominant. Thus, the DD mother in figure

produces F1 progeny that are dextral with a Dd genotype, and the dd mother produces progeny that are sinistral with the same Dd genotype. Moth Pigmentation In the flour moth, Ephestia kühniella, kynurenin, which is a precursor for pigment, accumulates in the eggs. The recessive allele, a, when homozygous, results in a lack

of kynurenin. Reciprocal crosses give different results for larvae and adults. When a non pigmented female is crossed with a pigmented male, the results are strictly Mendelian; but when the mother is pigmented (a+a), all the larvae are pigmented regardless of genotype.

The initial larval pigmentation comes from residual kynurenin in the eggs, which is then diluted out so that an adult’s pigmentation conforms to its own genotype.

Inheritance pattern of larval and adult pigmentation in the flour moth, Ephestia kühniella. A single locus controls the presence (a+) or absence (a) of kynurenin.

In the cross on the left, the mother is aa (nonpigmented). Her aa offspring, in both the larval and adult stages, are also nonpigmented. In the reciprocal cross (right), the mother has the a+a genotype and is pigmented. Her aa offspring are nonpigmented as adults but pigmented in larvae stage because of residual kynurenin from the egg, which eventually dilutes out because they were incapable of synthesizing their own kynurenine in the absence of dominant allele and hence loss of pigment in adult moth. Explanation (a+ )

Dark brown eyes and presence of pigment in other parts of the body in this moth are controlled by a dominant gene a+, responsible for production of a pigment precursor kynurenine. Homozygous recessive aa lacks kynurenine, so that it exhibits absence of pigment and the eyes therefore have red color. When heterozygote a+a (pigmented) is crossed to non pigmented homozygous recessive aa (aa ♀ x a+a ♂), as expected, progeny segregates 1 a+a : 1 aa, which phenotypically gives the ratio 1 pigmented : 1 non-pigmented. In the reciprocal cross, pigmented a+a (♀) x non-pigmented aa (♂), the progeny { 1a+a : 1 aa) had all the early larvae pigmented. In this case, however, when larvae ' matured, only half of them { a+a)were dark brown eyed, the other half (aa) were red eyed. These homozygous (aa)pigmented larvae received their egg cytoplasm from mother (a+a) and, therefore, had kynurenine in early stages of development, but they were incapable of synthesizing their own kynurenine in the absence of dominant allele and hence loss of pigment in adult moth.

EXAMPLES OF EXTRANUCLEAR INHERITANCE

The [poky] Mutant of Neurospora—Maternal Inheritance.

The fungus Neurospora crassa is an obligate aerobe; it requires oxygen to grow and survive, so mitochondrial functions are essential for its growth. The [poky] mutant grows much more slowly than the wild type. The mutant results from a change in the mtDNA, The [poky] mutant is defective in aerobic respiration as a

result of changes in the cytochrome complement of the mitochondria. The change in the cytochrome spectrum affects the ability of the mitochondria to generate sufficient ATP to support rapid growth, which explains the slow growth of the mutant. By using a strain to produce the protoperithecia (the female reproductive structure) as the female parent and conidia of another strain as a male parent, geneticists can make reciprocal crosses to determine whether any trait shows extranuclear inheritance. Compared with the conidia (the asexual spores), the protoperithecia have a large amount of cytoplasm. Thus they can be considered the female parent. Reciprocal crosses between [poky] and the wild type produce the following results:

all progeny show the same phenotype as the maternal parent, indicating maternal inheritance as a characteristic for the [poky] mutation. PETITE MUTATIONS IN YEAST

Under aerobic conditions, yeast grows with a distinctive colony morphology. Under anaerobic conditions, the colonies are smaller, and the structures of the mitochondria are reduced. Occasionally, when growing aerobically, small, anaerobic like colonies appear; but in these colonies, the mitochondria appear perfectly normal. These colonies are caused by petite mutations. All petites represent failures of mitochondrial function, they usually lack one or another cytochrome. When petites are crossed with the wild-type, three modes of inheritance emerge.

a. The segregational petite, caused by mutation of a chromosomal gene, exhibits Mendelian inheritance.

b. The neutral petite is lost immediately upon crossing to the wild-type. c. The suppressive petite shows variability in expression from one strain to the

next but is able to convert the wild-type mitochondria to the petite form.

In the first type called segregational petites when an individual is crossed with a normal strain, a 1 : 1 ratio of normal: petite results after segregation. This suggests Mendelian inheritance and the petite strain has originated due to a mutation in nuclear genes. Neutral petites seem to have mitochondria that entirely lack DNA. When neutral petites are crossed with the wild-type to form diploid cells, the normal mitochondria dominate. During meiosis, virtually every spore receives large numbers of normal mitochondria; the progeny are, therefore, all normal. Suppressive petites could exert their influence over normal mitochondria in one of two

ways. Suppressive petite mutants are found to have mutant DNA in their mitochondria. The suppressive mitochondria might simply out-compete the normal mitochondria and take over; they might simply reproduce faster within a cell. The suppressive petites when crossed to normal cells of yeast show the petite trait in the progeny but in non-Mendelian ratios. The mutant mitochondria replicate and transmit the mutant phenotype to the progeny cells. Antibiotic Influences Since the machinery of mitochondrial protein synthesis is prokaryotic in nature, antibiotics such as chloramphenicol and erythromycin can inhibit it. These antibiotics elicit a petite-type growth response in yeast. Antibiotic- resistant strains can be obtained

by growing yeast on the antibiotic; only resistant mutants will grow. The resistance appears to be inherited in the mitochondrial, not the cellular, DNA. A mitochondrial inheritance pattern results, with crosses between a resistant and a sensitive (wild-type) yeast. The resulting diploid colonies segregate both resistant and sensitive cells. The random sorting of mitochondria through cell division could result in a wild-type cell containing only sensitive mitochondria. Since some yeast have only one to ten mitochondria per cell, this random assortment of sensitive mitochondria can be expected to occur at a relatively high rate.

Extrachromosomal inheritance due to Chloroplast

Variegation in the four o’clock plant, Mirabilis jalapa. Or Plastid Inheritance in

Mirabilis jalapa Plastid inheritance means the inheritance of plastid characteristics due to plasma genes located in plastids. Plastid inheritance was first described by C. Corens (1908) in the four o’clock plant, Mirabilis jalapa. Variegation means the presence of white or yellow spots of variable size on the green background of leaves. Thus it forms the mosaic pattern of coloration on a leaf. Due to certain inheritable defects chloroplast of all cells or some cells of leaf often are unable to synthesize the chlorophyll pigments. Such cells remain non- green and form white or yellow colored leaf, or white or yellow patches, interspersed with areas containing normal green cells with healthy chloroplasts. Thus the leaves of Mirabilis jalapa may be green, white or variegated and some branches may have only green, only white or only variegated leaves.

Variegation may be produced by: (a) Some environmental factors, (b) Some nuclear genes, (c) Plasma-genes in some cases.

Since the first and second causes of leaf variegation do not concern cytoplasmic inheritance, the inheritance of variegation due to plasma-genes will be discussed here. C. Corens could predict color and variegation of offspring solely on the basis of the region of the plant on which the stigma parent was located. A flower from a white sector, when pollinated by any pollen, would produce white plants; a flower on a green sector or a variegated sector produced green or variegated plants, respectively, when pollinated by pollen from any region of a plant.

Since the bulk amount of cytoplasm containing many plastids is contributed by the egg and the male gametes contribute negligible amount of cytoplasm, therefore plastids present in the cytoplasm of egg is responsible for the appearance of maternal color in the offspring and the failure of male plant to transmit its color to offspring is reasonable. In the offspring from variegated female parents, green, white and variegated progeny are recovered in variable proportions. The variegated parent produces three kinds of

egg- some with colorless plastids, some contains only green plastids, and some are with both chloroplasts and leucoplasts. As a result, zygotes derived from these three types of egg cells will develop into green, white and variegated offspring’s, respectively. Uniparental Inheritance in Chlamydomonas Reinhardi

R. Sager (1970) and N. Gilham (1968) have reported some cases of extra-chromosomal inheritance in green alga Chlamydomonas reinhardi. The alga reproduces by asexual as well as sexual means. The sexual reproduction takes place by fusion between two morphologically similar but physiologically dissimilar haploid gametes coming from different haploid parents designated as ‘+’ and ‘-‘. Although both the sexes contribute equally to the zygote, there is maternal transmission of certain cytoplasmic traits. Chlamydomonas is a haploid unicellulate green alga. Chlamydomonas does not have sexes but does have mating types +and - . Only individuals of opposite type can mate. The two mating types are governed by two alleles of a nuclear single gene. The alleles are named as mt+ and mt–. The + mating type is considered as female, while the – mating type is

regarded as male. During sexual reproduction one mt+ and one mt– cell pair and fuse together to form a zygote where there is mixture of cytoplasm coming from both mt+ and mt– gametes. The zygote undergoes meiosis to produce 4 haploid meiozoospores of which two zoospores contain ‘+’ alleles and other two contain ‘-‘ alleles, i.e., it shows typical 1 : 1 segregation for nuclear genes. But for their plasma genes all zoospores are identical and contain only mt+ type plasma genes by mt+ plasma genes. R. Sager isolated two strains of Chlamydomonas: one strain was resistant (Sr) to streptomycin and the other one is sensitive.

The trait of streptomycin resistance is believed to be located in its cp-DNA (chloroplast DNA). Mating between mt+ streptomycin resistant (Sr) and mt sensitive (Ss) cells produce only resistant progeny. But the reciprocal cross between mt+ susceptible and mt– resistant shows again the expected segregation for mating type but all progenies are sensitive type. Therefore, it clearly provides an example for extra-nuclear inheritance.

Infective Particles or Kappa Particles in Paramecium: Paramecium Tracy Sonneborn discovered the killer trait in Paramecium. In 1943, T. M. Sonneborn reported that some strains of P. aurelia contain kappa particles and are known as killer strain. Kappa particles are the symbiont bacteria called Caedobacter taeniospiralis. The diameter of kappa particles are about 0.2µ. They are bounded by a membrane and contain a little bit of cytoplasm with DNA. The strain of Paramecium in which the kappa particles are absent are called sensitive strain. The sensitive strains are killed by the killer strain.

There are two types of strains in Paramecium. One has kappa particles in its cytoplasm and other does not have such particles. The presence of kappa particles in the cytoplasm leads to production of a toxin known as paramecin. This toxin can kill the strain of Paramecium which lacks kappa particle. Thus, the strain with kappa particle is known as killer strain and that without kappa particle is called as sensitive strain. Multiplication of kappa particles in the cytoplasm takes place by fission. However, their multiplication is governed by a dominant nuclear gene (K). They can multiply in the homozygous dominant (KK) or heterozygous (Kk) individuals. Kappa particles cannot multiply in recessive (kk) individuals. Even if kappa particles are introduced into kk strains, they will gradually disappear due to their inability to multiply and the strain will become sensitive. Though the multiplication of kappa particles is dependent on nuclear genes, their action is independent of nuclear gene. The inheritance of kappa particles can be studied by conjugation between killer and sensitive strains. The conjugation may be of two types, viz: a. Short duration conjugation and b. Long duration conjugation.

The consequences of such conjugations are given below: (a) Short Duration Conjugation: Short duration conjugation leads to exchange of nuclear genes between the killer and sensitive strains. Exchange of cytoplasm does not take place in such conjugation. Thus, the ex-conjugants (resultant strains) will be heterozygous (Kk) for killer gene. However, the strain with killer cytoplasm produces killer (KK) and sensitive (kk) strains by further division, whereas the sensitive stain produces only sensitive strains (kk) by

further division. This clearly indicates that the killer character is not governed by nuclear gene. (b) Long Duration Conjugation: Such conjugation between killer and sensitive strains leads to exchange of both nuclear genes as well as cytoplasm. Here both the ex-conjugants are heterozygous (Kk) but killer. Autogamy of both the ex-conjugants produces killer and sensitive strains in 1 : 1 ratio. This has demonstrated that kappa particles have cytoplasmic inheritance Summary on Paramecium T. M. Sonneborn described the inheritance of some cytoplasmic particles known

as kappa and their relation to nuclear gene in the common cillate protozoan, Paramecium aurelia.

There are two strains of Paramecium. They are killer and sensitive. Killer strain produces a toxic substance called paramecin that is lethal to other

individuals called "sensitive’s" . The production of paramecin in killer type is controlled by certain cytoplasmic

particles known as kappa particles. The sensitive strains lack these particles. The kappa particles are transmitted through the cytoplasm. The existence, production and maintenance of kappa particles are controlled by

a dominant gene ‘K’ present in the nucleus. However, ‘K’ cannot initiate the production of kappa in the total absence of kappa in the cytoplasm.

When a Paramecium of killer strain is having the genotype “KK” or (K+) conjugates with the Paramecium of non-killer strain having the genotype “kk”, the exconjugants are all heterozygous for “Kk” genes.

The development of a particular type depends upon the duration of cytoplasmic exchange If conjugation is normal, i.e., lasts only for a short time, and no exchange

of cytoplasm takes place between the two, both killers and non-killers (sensitive) are produced.

However in rare or prolonged conjugation (i.e., lasting for long time) the cytoplasmic bridge between the two conjugants is larger. In such cases, in addition to the nuclear material, the cytoplasmic materials are also exchanged.

During this cytoplasmic exchange, the kappa particles present in the cytoplasm of the killer type enter the non-killer type and convert it into a killer type. So all the offspring produced by the exconjugants are killer type.

Sigma Particle in Drosophila:

In Drosophila, two types of flies are found with regard to C02 sensitivity. Some flies are

sensitive to C02 exposure and some are fairly resistant. The sensitive flies become

immobile when they are exposed to C02 concentration and may even die sometimes.

A cross between sensitive female and normal male produced all sensitive individuals in

F1. The reciprocal cross (normal female x sensitive male) produced all normal offspring

in F1 ). This suggested that CO2 sensitivity is inherited through the cytoplasm.

Investigation using electron microscopes have demonstrated that a virus like particle

called sigma is responsible for sensitivity to CO2 in Drosophila.

The high degree of C02– sensitivity is associated with the presence of a DNA virus

called sigma factor found in the cytoplasm of C02 sensitive Drosophila.

Sigma factor is transmitted through the egg cytoplasm. When a cross is made between

C02– sensitive female with normal male, all offspring’s are C02 sensitive. Again, in

reciprocal cross, i.e., a cross between normal female and C02 sensitive male, most of

the offspring’s are normal except for a small proportion of progeny which are

C02 sensitive. Therefore, the inheritance pattern of C02sensitivity is non-Mendelian and

confirms the cytoplasmic basis of inheritance.

RNA Viruses in Fungi:

Like Paramoecium, there are two strains of yeast (Saccharomyces cerevisial). One

strain is killer and other one is sensitive. The hiller strain secretes a proteinaceous toxic

substance that kills the sensitive strain of yeast cell.

When a cross is made between killer and sensitive strain of yeast, only killer offspring’s

are produced—indicating uniparental inheritance. There are some other strains of yeast

which are called neutral strains.

Neutral strains are neither killed by killer nor do they kill the sensitive strain. But the

cytoplasm of both killer and neutral strains contain two types of double-stranded RNA in

the form of isometric virus-like particles (about 39 nm in diameter).

The existence and maintenance of virus particles in the yeast cytoplasm are controlled

by some dominant nuclear genes called MAK genes (maintenance of killer). Some other

nuclear genes—e.g., KEXx (killer expression) and KEX2—convert killers into neutrals.

A similar situation is noted is case of Ustilago maydis, a maize smut fungus. Here the

cytoplasm of killer strain also contains maycovirus like particle containing double-

stranded RNA. Killer strain secretes a toxin which kills sensitive strains but it has no

lethal effect on resistant strains. Resistant strains are particularly resistant to one of the

killer strains designated as p1, p4 and p6. Some nuclear genes denoted as Pr1,Pr

4 and

pr6 convert sensitive strain into resistant ones.

In all such cases mentioned above, the virus like particles are not the integral part of the

normal cellular organisation but their existence and transmission indirectly provides

some evidences in favour of cytoplasmic inheritance.

Human Genetic Diseases and Mitochondrial DNA Defects.

A number of human genetic diseases result from mtDNA gene mutations. These

diseases show maternal inheritance.

The following are some brief examples.

• Leber’s hereditary optic neuropathy (LHON). This disease affects midlife adults and

results in complete or partial blindness from optic nerve degeneration. Mutations in the

mitochondrial genes for eight electron transport chain proteins, and ATPase 6, all lead

to LHON. The electron transport chain drives cellular ATP production by oxidative

phosphorylation. It appears that death of the optic nerve in LHON is a common result of

oxidative phosphorylation defects, here brought about by inhibition of the electron

transport chain.

• Kearns-Sayre syndrome.

People with this syndrome have three major types of neuromuscular defects:

1. progressive paralysis of certain eye muscles,

2. abnormal accumulation of pigmented material on the retina leading to chronic

inflammation and degeneration of the retina

3. heart disease.

The syndrome is caused by large deletions at various positionsin the mtDNA. One

model is that each deletion removes one or more tRNA genes, so mitochondrial protein

synthesis is disrupted. In some unknown way, this leads to development of the

syndrome.

• Myoclonic epilepsy and ragged-red fiber (MERRF) disease. Individuals with this

disease exhibit “ragged-red fibers,” an abnormality of tissue when seen under the

microscope. The most characteristic symptom of MERRF disease is myoclonic seizures

(sudden, short-lived, jerking spasms of limbs or the whole body). Other principal

symptoms are ataxia (defect in movement coordination) and the accumulation of lactic

acid in the blood. The disease is caused by a single nucleotide substitution in the gene

for a lysine tRNA. The mutated tRNA adversely affects mitochondrial protein synthesis,

and somehow this gives rise to the various phenotypes of the disease.