Textbook assignment: Chapter 18, Pages 549 - 577. These notes also describe studies on evolution of human mitochondrial DNA (textbook pages 651-652) and maternal effect genes (textbook pages 688-689).
Major concepts:
Non-Mendelian inheritance: This lecture deals with various types of control over phenotype by genetic systems other than the genes that are present in the nuclear genome of the individual. The sequence of presentation differs somewhat from that in the textbook. The first section briefly introduces the concept of independent gemones in cellular organelles such as mitochondria and chloroplasts. This is followed by a more detailed description of the mitochondrial genome and patterns of inheritance of mitochondrial genes. The nest major section describes the genomes of chloroplasts and genetic effects caused by cytoplasmic plasmids. This is followed by a brief description of other non-nuclear patterns of inheritance, some of which are not described in the textbook. The final part of the lecture deals with maternal effect, in which the maternal genome determines the phenotype of the progeny, without any direct contribution from the genome of the progeny.
Organelle genomes: Chloroplasts and mitochondria both contain DNA that codes for some, but not all of their functions. The presence of these independent genomes results in some unusual patterns of inheritance. Names that have been applied to such inheritance include extranuclear, cytoplasmic, uniparental, and non-Mendelian. Section 18.1 of the textbook presents a substantial amount of information about the structure and metabolic functions of chloroplasts and mitochondria. You are encouraged to read through this material, but you will not be required to understand it beyond the level presented in these notes. These topics are covered at an introductory level in MCDB 1150 and at a far more advanced level in MCDB 3120.
Mitochondrial DNA: Mitochondrial DNA is circular, with no associated histones, and typically has a GC/AT ratio different from that of the nuclear DNA in the same species. The size varies with the species. In humans, the DNA is 16,569 bp in length (around a closed circle), whereas in yeast, the size is about 84kb. In some plants, the size may range up to 200kb. Each mitochondrion normally contains multiple copies of the mtDNA, whose total amount per cell is typically in the range of 40 to 2,000 copies. Mitochondria are dynamic structures that fuse and break. Recombination is known to occur among the mtDNAs within a cell.
Possible prokaryotic origins: Mitochondrial DNA (as well as that of chloroplasts) is believed to have arisen from prokaryotic symbionts. Mitochondrial DNA and a number of the aspects of mitochondrial gene expression resemble those of bacteria. In particular, protein synthesis that occurs inside of mitochondria is not inhibited by cycloheximide, which inhibits eukaryotic protein synthesis, but not bacterial protein synthesis. It is widely believed that prokaryotic cells were the first to achieve aerobic metabolism, and that symbiotic incorporation of such bacteria confered aerobic capacity on early eukaryotic organisms. Even today, mitochondria remain the organelle solely responsible for aerobic metabolism.
Mitochondrial genes: Because of their small sizes, mitochondrial genomes carry only a small fraction of the genes needed for mitochondrial function. The remainder of the needed genes are found in the nuclear genome. Since RNA cannot readily be imported into mitochondria, all of the RNA molecules needed for translation are coded from the mitochondrial genome, including both ribosomal RNAs and transfer RNAs. A few enzymes involved in mitochondrial function are also coded from the mitochondrial genome, but many other mitochondrial proteins are coded from the nuclear genome and imported into the mitochondria after cytoplasmic translation. A specific signal sequence on the proteins appears to be needed for import into the mitochondria. All of the enzymes involved in mitochondrial transcription and protein synthesis are imported from the cytoplasm, including mitochondrial RNA polymerase, ribosomal proteins, and aminoacyl-tRNA synthetases. The organization of the human mitochondrial genome 1s described in figure 18.12.
Altered genetic code in mitochondria: One other interesting feature of mitochondrial genetics is that there are several codons that are read differently in mitochondria than in cytoplasmic translation. These differences are briefly mentioned page 106 of our textbook. Last year's textbook (Klug and Cummings, Concepts of Genetics, 5th Edition, available at Norlin Reserve) provided a more detailed description on pages 334-335 and in table 12.5. The modifications of the code that occur in mitochondria differ among different types of eukaryotic organisms.
Mitochondrial inheritance in budding yeast: When a diploid yeast cell is formed by fusion of two haploid strains with genetic differences in their mitochondria, both types of mitochondria are initially present in roughly equal numbers. Such a cell is considered to be heteroplasmic because it contains two different types of mitochondria. However, as shown in figure 18.14, only a few mitochondria are passed to the daughter cell each time that budding occurs. By random chance cells frequently receive only one type and become homoplasmic. This is an irreversible process, and over a relatively short period of time virtually all of the cells become homoplasmic, containing only one or the other of the two parental types of mitochondria (figures 18.15 and 18.16).
Aerobic and anaerobic metabolism in yeast: Yeast have highly adaptable metabolic patterns. Under fully aerobic conditions, they are able to metabolize glucose to carbon dioxide and water. This requires a process of aerobic metabolism known as the citric acid cycle, which occurs in the mitochondria. Under anaerobic condition, yeast are still able to use glucose as an energy source. However, in this case, the end products are ethanol and carbon dioxide, and there is no net oxidation of the glucose. This type of metabolism is called fermentation and occurs entirely in the cytoplasm.
Petite mutations in yeast: In the late 1940's, Boris Ephrussi and his colleagues discovered that under aerobic conditions, there were occasional colonies of yeast that grew much more slowly. These were named petite because they formed small colonies at a time when the regular strain (grande) had already formed large colonies. Petite mutations were found to make small colonies because they were incapable of aerobic metabolism, which suggested a mitochondrial defect. In crosses with grande strains, many of the petite mutations did not behave as expected from Mendelian genetics. The non-Mendelian inheritance was originally attributed to an unknown cytoplasmic factor designated rho (normally written as the Greek letter rho, but that option is not available in html). After discovery of the mitochondrial genome, it was found that the non-Mendelian petite mutations were due to changes in the mitochondrial DNA. However, the symbol rho has continued to be used.
Classes of petite mutations: Petite mutations have been divided into three classes:
Segregational petites, also known as nuclear petites, are caused by mutations in the nuclear genome, and are inherited in a Mendelian manner, as expected for unicellular organisms with a sexual cycle. As noted above, mitochondrial function is dependent on nuclear genes as well as mitochondrial genes.Neutral petites behave initially as recessive mutations in crosses that form diploid strains. However, when meiosis occurs to restore haploid nuclear genomes, all four of the progeny strains are grande. This uniparental pattern of inheritance does not fit a normal Mendelian expectation. The neutral petites, which are sometimes designated rho0, totally lack a mitochondrial genome. Thus, the only mitochondria that are able to function in the progeny of a cross with a neutral petite are derived from the grande parent. Because mitochondria replicate independently and are present in substantial numbers per cell, each of the four progeny receives normal mitochondria from the grande parent.
Suppressive petites (designated rho-) exhibit somewhat variable behavior, depending on the strain, but there is either partial or complete suppression of the grande pattern of growth in all or most of the meiotic segregants. Suppressive strains have retained a small part of the mitochondrial genome and are somehow able to inactivate the wild-type genome. There are two theories of how this works. One is that the partial genome, which cannot support mitochondrial function, reproduces more rapidly than the much larger complete gemone and thus displaces the full genome. A second theory suggests that suppressive petite genomes undergo extensive recombination with wild-type genomes, introducing defects into the wild-type genomes that render them inoperable. There is also a slow-growing poky mutation in Neurospora, which behaves very much like the suppressive petitie in yeast and probably has a similar mechanism for displacement of the normal mitochondrial genome.
Mitochondrial recombination: Mitochondria in yeast (and other species are capable of fusing, which can bring two different mitochondrial genomes within the same mitochondrion. Recombination has been demonstrated to occur, but is sufficiently rare so that it is difficult to use for genetic mapping.
Mitochondrial inheritance in animals: In animal systems where a small sperm cell fertilizes a large egg cell, the sperm mitochondria normally do not enter the egg cytoplam. This generates a pattern of inheritance that is almost exclusively maternal and is commonly referred to as uniparental-maternal inheritance. However, as shown in boxed example 18.2, a small amount of paternal inheritance can be demonstrated when special steps are taken to see it.
Human mitochondrial diseases: Several human diseases are known that are transmitted maternally as defects in the mitochondrial genome, as described in the textbook. Because each cell contains numerous mitochondria, varying mixtures of mutant or partially deleted mitochondria often exist in cells that also contain normal mitochondria. This condition is known as heteroplasmy. Mitochondrial defects have also been implicated in some cases of Alzheimer's disease, and possibly also in aging, although the latter remains highly controversial.
Evolution of human mitochondrial DNA: Because of its relatively small size and rapid rate of evolution, the mitochondrial genome is useful for studies of recent evolution. In addition, in many animal species, including humans, sperm mitochondria are mostly rejected from the zygote at the time of fertilization, such that all mitochondria in progeny of both sexes are derived from the ovum. This results in a primarily maternal pattern of inheritance, with very little mixing or assortment of genomes. This combination of properties makes it easy to look at evolutionary trends among closely related species, or even among races within a single species.
Eve: Although the studies have remained controversial, comparisons of mitochondrial DNA from various human races and ethnic groups have led to construction of a proposed human evolutionary tree. One widely quoted study that examined RFLP patterns and assumed strictly maternal inheritance suggested that all modern humans were descended from the progeny of one woman who lived in Africa about 200,000 years ago. This did not necessarily mean she was the only woman alive at the time. However, there must have been some sort of "bottleneck" situation in which only a very few early humans survived (perhaps a severe epidemic), with all of the survivors being descended from one ancesteral female. More recent studies that have examined other parts of the human mitochondrial genome and allowed for a limited amount of paternal inheritance have offered somewhat different interpretations, but there is general agreement on an African origin and a founder genotype within the last 800,000 years or less. This concept is discussed briefly on pages 651-652 of our current textbook.
Patterns of uniparental inheritance: Uniparental inheritance of mitochondrial genomes can occur in several distinctly different ways.
Chloroplast genomes: All photosynthesis in higher plants occurs in cellular organelles known as chloroplasts, which are generally thought to have evolved from symbiotic cyanobacteria (prokaryotic blue-green algae). Like mitochondria, chloroplasts have their own circular genomes that code for components of their protein-synthesizing machinery, as well as subunits of photosynthetic protein complexes. The study of cytoplasmic inheritance in plants is complicated by the presence in plant cells of both mitochondria and chloroplasts. Because both of these organelles appear to have prokaryotic origins and similar patterns of gene expression, it is sometimes difficult to determine which is responsible for a particular cytoplasmic inheritance phenomenon.
Patterns of inheritance in chloroplasts: Normal chloroplasts are light-responsive and revert to smaller forms without chlorophyll called proplastids in the absence of light. Genetically defective chloroplasts often fail to respond to light, causing the presence of spots or stripes that lack chlorophyll on leaf surfaces or other areas of the plant. In the simplest cases, there is clearly defined maternal inheritance. Thus, for example, a flower from a white part of a four-o'-clock plant will produce white progeny no matter what pollen it is fertilized with, and a flower from a green area will always produce a green plant, irrespective of the pollen. Variegated plants with areas of white and green typically arise from heteroplasmic ovules. There are also some plants in which the chloroplasts are paternally inherited (from the pollen-producing parent), and in some other cases the inheritance is biparental. Also, as described boxed example 18.4, all of these mechanisms can operate concurrently in some species. In Chlamydomonas, chloroplast DNA from the minus mating type is selectively destroyed together with the destruction of mitochondrial DNA from the plus mating type described above.
Killer strains of Paramecium: Certain stocks of the ciliated protozoan, Paramecium aurelia, contain infective particles that render the "killer" strains capable of killing "sensitive" strains. These are of two types, kappa particles, which cause the release of a toxin that kills senstive strains, and mu particles (not discussed in the textbook), which kill mates during conjugation (a primitive type of sexual exchange that occurs in Paramecium). In both cases, the killer particles are bacteria-like and require interactions with nuclear genes to be maintained. In addition, the kappa particles appear to release their toxin only when infected by a particular type of bacteriophage.
Altered sex ratios in Drosophila: In Drosophila, there exists an infectious condition where very few male progeny are formed and the trait is passed exclusively to daughters. The causative agent in this case appears to be a spirochete, which can be isolated and infected into other females, causing the trait. Current data suggests that the toxic agent is a virus carried within the bacteria in the females.
Prokaryotic plasmids: Although prokaryotic cells do not have a separate nucleus, plasmids have a relationship to the primary bacterial genome that is similar in principle to the relationship between extranuclear and nuclear genomes in eukaryotic cells (pages 183-184). We have already seen plasmids that confer antibiotic resistance, as well as the F+ fertility factor for bacterial conjugation, and a variety of genetically engineered plasmids that are used as cloning vectors.
Maternal effect genes: Section 18.7 describes cases of apparent uniparental-maternal ihheritance that are not cytoplasmic in their origin, but instead are determined by the nuclear genotype of the mother. . In both vertebrate and invertebrate animals, fertilization introduces a haploid sperm nucleus (and very little else) into an egg cell that contributes a both a haploid maternal nucleus and large mass of cytoplasm to the zygote. The maternal origin of the cytoplasm of the fertilized egg, together with the almost complete exclusion of the non-nuclear parts of the sperm, generates a newly formed zygote that contains substantial amounts of maternally-derived proteins and mRNA that are not balanced by comparable paternal contributions. These maternally-derived materials can have a major influence on early stages of embryonic development.
bicoid as an example of a maternal-effect gene: Because of the contribution of maternally-derived mRNA and proteins to early embryonic development, the phenotypic traits of the embryos are sometimes determined by the genotypes of their mothers, rather than by their own genotypes. One example of this is the bicoid gene in Drosophila, whose protein product is strictly required for normal development of anterior (head-end) structures (described on pages 688-689 of our current textbook). The mRNA for the bicoid protein is deposited into the anterior end of the egg from nurse cells that surround the egg during its development. Mating of two flies that are heterozygous for lack of a functional bicoid gene will result in 1/4 of their embryos being homozygous for loss of bicoid function. Although those embryos are unable to code for their own bicoid protein, they nevertheless develop normally because of the presence of maternally-derived bicoid mRNA in the eggs. However female flies that are homozygous for lack of functional bicoid genes produce eggs with no bicoid mRNA. Embryos derived from these eggs fail to develop anterior structures even when the eggs are fertilized with sperm that introduce a fully functional allele of the bicoid gene into the zygote nucleus. Thus, bicoid is a strict maternal-effect gene (page 688 of textbook).
Coiling of snail shells: A classically studied case of maternally-determined phenotypic expression is the coiling of the shell of the pond snail Limnaea peregra. The spiral coiling of the shell can be either dextral or sinstral, with dextral dominant in heterozygotes. However, it is the genotype of the mother, and not that of the developing embryo that determines the spiral pattern. Thus, a Dd mother will always produce progeny with dextral spirals, even when the genotype of the progeny is dd. Similarly, a dd mother will always produce progeny with sinstral spirals, even when the progeny are Dd. The pattern of spiraling of the shell is determined by the pattern of the earliest cleavage divisions in the embryo, which in turn is determined by the mother's genotype, and ultimately by the presence of the gene product coded by the D allele. Thus, the direction of the spiral is another example of a maternal effect on phenotype that is dominant over the genotype of the progeny (pages 572-573 and figure 18.21).
Additional examples of maternal effect genes: Those of you who take MCDB 4650 (Developmental Biology) will encounter many additional examples in which it is the genotype of the mother, rather than the genotype of the embryo, that determines the phenotype of the embryo, particularly during earlier stages of embryonic development.