Textbook assignment: Chapter 8, pages 208-220. Please note that the order of presentation of topics in these notes and the classroom lecture has been rearranged somewhat from the order in the textbook.
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 first part of the lecture deals with maternal effects. The next major section describes the independent genome carried within each mitochondrion in eukaryotic cells and the final sections describe the genomes of chloroplasts and genetic effects caused by cytoplasmic plasmids.
Maternal origin of zygote cytoplasm: 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 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, as discussed in the first part of this lecture. In addition, all of the mitochondria in the zygote are of maternal origin. Thus, inheritance of mitochondrial genes is exclusively maternal, with no paternal contribution.
bicoid as an example of maternal-effect genes: 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. 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 210 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 209-210 and figure 8.2).
Moth larval pigmentation: Yet another example of maternal effects is pigmentation of larva of the flour moth, Ephestia kuhniella. In this case, a biochemical precursor for pigment formation, kynurenin, accumulates in the egg and is converted to pigment during early larval development, irrespective of the pigmentation genes that the larva carries. In this case, the maternally-derived pigmentation is gradually diluted with growth, such that the adult exhibits pigmentation determined by its genes (page 209 and figure 8.1).
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.
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. In this portion of the lecture, we will examine examples of mitochondrial inheritance.
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 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, the RNA molecules needed for translation are all 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 and function of the mitochondrial genome are described in greater detail on pages 494-495 of the textbook, and will be discussed in lecture 33. One other interesting feature of mitochondrial genetics is that there are several codons that are read differently in mitochondria than in cytoplasmic translation. We will examine that topic in lecture 24 (textbook pages 334-335, table 12.5).
Mitochondrial and cytoplasmic 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.
poky muitations in Neurospora: The slow-growing poky mutation in Neurospora behaves very much like the suppressive petitie in yeast. In simple crosses, it behaves as if "maternally" inherited, with the phenotype of the progeny totally dependent on the mitochondrial genotype of the parent that supplies the cytoplasm-rich Protoperithecium (Figure 7.10). However, the more interesting situation occurs when vegetative hyphae from two strains are fused to give rise to heterokaryons (this term refers to having two different types of nuclei, but in this case, there are also two types of cytoplasm, and thus two types of mitochondria). Growth rate initially seems normal, but there is a progressive slowing of growth and loss of normal mitochondrial function, with the poky phenotype gradually becoming dominant. It appears that the normal mitochondria are gradually displaced or inactivated by poky mitochondria. Thus, poky is another example of the broader category of suppressive mutations.
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 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 strictly maternal pattern of inheritance, with no 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. Current analysis suggests that all modern humans have descended from the progeny of one woman who lived about 200,000 years ago. This does 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. This concept is discussed briefly on page 699 of our current textbook.
Patterns of uniparental inheritance: Uniparental inheritance of mitochondrial genomes can occur in at least three 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. However, there are also complex patterns of interaction between nuclear genes and chloroplasts, such that certain nuclear mutations tend to "turn off" the chloroplasts, as in the effect of the iojap gene on patterns of chlorophyl expression in corn (pages 211-212 and figure 8.3 in the textbook). Because of the complexity of this system and the fact that its mechanisms are not fully understood, we will not explore it in detail.
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. The textbook also describes another extranuclear agent that causes unusual sensitivity to carbon dioxide in Drosophila.
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. We have already seen an example of a prokaryotic plasmid in the F+ fertility factor for bacterial conjugation. Additional types of bacterial plasmids were also described in Chapter 6 (pages 158-160). These include plasmids that transfer multiple antibiotic resistance from one cell to another and others that are responsible for the production of proteins called colicins that make certain strains of bacteria toxic to other strains. Later in the semester, we will deal extensively with the use of bacterial plasmids of the antibiotic resistance type as gene-cloning vectors.