1. COMSATS INSTITUTE OF INFORMATION TECHNOLOGY<br />Developmental Genetics <br /> <br />Zulkifal Yousaf<br /> <br />DEVELOPMENTAL GENETICS:-<br /> <br /> Every multicellular organism begins life as a unicellular, fertilized egg. This single-celled zygote undergoes repeated cell divisions, eventually producing millions or trillions of cells that constitute a complete adult organism. Initially, each cell in the embryo is totipotent—it has the potential to develop into any cell type. Many cells in plants and fungi remain totipotent, but animal cells usually become committed to developing into specific types of cells after just a few early embryonic divisions. This commitment often comes well before a cell begins to exhibit any characteristics of a particular cell type; once the cell becomes committed, it cannot reverse its fate and develop into a different cell type. A cell becomes committed by a process called determination, the mechanism of which is still unknown. For many years, the work of developmental biologists was limited to describing the changes that take place in the course of development, because techniques for probing the intracellular processes behind these changes were unavailable. But, in recent years, powerful genetic and molecular techniques have had a tremendous influence on the study of development. In a few model systems such as Drosophila, the molecular mechanisms underlying developmental change are now beginning to be understood.<br /> The Genetics of Pattern Formation in Drosophila:-<br /> One of the best-studied systems for the genetic control of pattern formation is the early embryonic development of Drosophila melanogaster. Geneticists have isolated a large number of mutations in fruit flies that influence all aspects of their development, and these mutations have been subjected to molecular analysis, providing much information about how genes control early development <br /> <br />Stages in the development and the genes that control that stages:-<br />Stages in the early development o in the early development of<br />fruit flies and Developmental Stage Genes<br />Establishment of main Egg polarity genes<br />body axes<br />Determination of number and Segmentation genes<br />polarity of body segments<br />Establishment of identity Homeotic genthe genes that control<br />of each segmentage and the genes that control<br />each stage<br /> The development of the fruit fly :-<br /> <br /> An adult fruit fly possesses three basic body parts: head, thorax, and abdomen.The thorax consists of three segments: the first thoracic segment carries a pair of legs; the second thoracic segment carries a pair of legs and a pair of wings; and the third thoracic segment carries a pair of legs and the halteres (rudiments of the second pair of wings found in most other insects). The abdomen contains nine segments. When a Drosophila egg has been fertilized, its diploid nucleus immediately divides nine times without division of the cytoplasm, creating a single, multinucleate cell. These nuclei are scattered throughout the cytoplasm but later migrate toward the periphery of the embryo and divide several more times. Next, the cell membrane grows inward and around each nucleus, creating a layer of approximately 6000 cells at the outer surface of the embryo . Four nuclei at one end of the embryo develop into pole cells, which eventually give rise to germ cells. The early embryo then undergoes further development in three distinct stages:<br /> (1) the anterior–posterior axis and the dorsal–ventral axis of the embryo are established<br /> (2) the number and orientation of the body segments are determined<br /> (3) the identity of each individual segment is established<br /> Different sets of genes control each of these three stages <br />Egg-polarity genes :-<br /> <br />The egg-polarity genes play a crucial role in establishing the two main axes of development in fruit flies. You can think of these axes as the longitude and latitude of development: any location in the Drosophila embryo can be defined in relation to these two axes. There are two sets of egg-polarity genes: one set determines the anterior–posterior axis and the other determines the dorsal–ventral axis. These genes work by setting up concentration gradients of morphogens within the developing embryo. A morphogen is a protein whose concentration gradient affects the developmental fate of the surrounding region. The egg-polarity genes are transcribed into mRNAs during egg formation in the maternal parent, and these mRNAs become incorporated into the cytoplasm of the egg. After fertilization, the mRNAs are translated into proteins that play an important role in determining the anterior–posterior and dorsal–ventral axes of the embryo.<br />Because the mRNAs of the polarity genes are produced by the female parent and influence the phenotype of their offspring, the traits encoded by them are examples of genetic maternal effects. Egg-polarity genes function by producing proteins that become asymmetrically distributed in the cytoplasm, giving the egg polarity, or direction. This asymmetrical distribution may take place in a couple of ways. The mRNA may be localized to particular regions of the egg cell, leading to an abundance of the protein in those regions when the mRNA is translated. Alternatively, the mRNA may be randomly distributed, but the protein that it encodes may become asymmetrically distributed, either by a transport system that delivers it to particular regions of the cell or by its removal from particular regions by selective degradation.<br />Determination of the dorsal–ventral axis:- <br /> The dorsal– ventral axis defines the back (dorsum) and belly (ventrum) of a fly. At least 12 different genes determine this axis, one of the most important being a gene called dorsal. The dorsal gene is transcribed and translated in the maternal ovary, and the resulting mRNA and protein are transferred to the egg during oogenesis. In a newly laid egg, mRNA and protein encoded by the dorsal gene are uniformly distributed throughout the cytoplasm but, after the nuclei migrate to the periphery of the embryo Dorsal protein becomes redistributed. Along one side of the embryo, Dorsal protein remains in the cytoplasm; this side will become the dorsal surface. Along the other side, Dorsal protein is taken up into the nuclei; this side will become the ventral surface. At this point, there is a smooth gradient of increasing nuclear Dorsal concentration from the dorsal to the ventral side .<br /> The nuclear uptake of Dorsal protein is thought to be governed by a protein called Cactus, which binds to Dorsal protein and traps it in the cytoplasm. The presence of yet another protein, called Toll, can alter Dorsal, allowing it to dissociate from Cactus and move into the nucleus. Together, Cactus and Toll regulate the nuclear distribution of Dorsal protein, which in turn determines the dorsal–ventral axis of the embryo.<br /> Inside the nucleus, Dorsal protein acts as a transcription factor, binding to regulatory sites on the DNA and activating or repressing the expression of other genes. High nuclear concentration of Dorsal protein (as on the ventral side of the embryo) activates a gene called twist, which causes mesoderm to develop. Low concentrations of Dorsal protein (as in cells on the dorsal side of the embryo), activates a gene called decapentaplegic, which specifies dorsal structures. In this way, the ventral and dorsal sides of the embryo are determined.<br />0 hours<br />2 days<br />3 days<br />5 days<br />9 days<br />5–8 Dorsal protein in the nuclei helps to determine the dorsal–ventral axis of the Drosophila embryo. (a) Relative concentrations of Dorsal protein in the cytoplasm and nuclei of cells in<br />the early Drosophila embryo. (b) Micrograph of a cross section of the embryo showing the Dorsal protein, darkly stained, in the nuclei along the ventral surface<br /> <br /> Determination of the anterior–posterior axis :-<br /> Establishing the anterior–posterior axis of the embryo is a crucial step in early development.We will consider several genes in this pathway. One important gene is bicoid, which is first transcribed in the ovary of an adult female during oogenesis. Bicoid mRNA becomes incorporated into the cytoplasm of the egg and, as it is passes into the egg, bicoid mRNA becomes anchored to the anterior end of the egg by part of its 3_ end. This anchoring causes bicoid mRNA to become concentrated at the anterior end (number of other genes that are active in the ovary are required for proper localization of bicoid mRNA in the egg.) When the egg has been laid, bicoid mRNA is translated into Bicoid protein. Because most of the mRNA is at the anterior end of the egg, Bicoid protein is synthesized there and forms a concentration gradient along the anterior–posterior axis of the embryo, with a high concentration at the anterior end and a low concentration at posterior end. This gradient is maintained by the continuous synthesis of Bicoid protein and its short half-life. The high concentration of Bicoid protein at the anterior end induces the development of anterior structures such as the head of the fruit fly. Bicoid—like Dorsal—is a morphogen. It stimulates the development of anterior structures by binding to regulatory sequences in the DNA and influencing the expression of other genes. One of the most important of the genes stimulated by Bicoid protein is<br />hunchback, which is required for the development of the head and thoracic structures of the fruit fly.<br />The development of the anterior–posterior axis is also greatly influenced by a gene called nanos, an egg-polarity gene that acts at the posterior end of the axis. The nanos gene is transcribed in the adult female, and the resulting mRNA becomes localized at the posterior end of the egg . After fertilization, nanos mRNA is translated into Nanos protein, which diffuses slowly toward the anterior end. The Nanos protein gradient is opposite that of Bicoid protein: Nanos is most concentrated at the posterior end of the embryo and is least concentrated at the anterior end. Nanos protein inhibits the formation of anterior structures by repressing the translation of hunchback mRNA. The synthesis of the Hunchback protein is therefore stimulated at the anterior end of the embryo by Bicoid protein and is repressed at the posterior end by Nanos protein. This combined stimulation and repression results in a Hunchback protein concentration gradient along the anterior–posterior axis that, in turn, affects the expression of other genes and helps determine the anterior and posterior structures.<br /> <br />of the dorsal–ventral axis in<br />fruit flies and their actiTn tt anterior–posterior axis in a Drosophila embryo is<br />determined by concentrations of Bicoid and Nanos proteins<br />Segmentation genes:- <br />The fruit fly has segmented body plan. When the basic dorsal–ventral and anterior–posterior axes of the fruit-fly embryo have been established, segmentation genes control the differentiation of the embryo into individual segments. These genes affect the number and organization of the segments, and mutations in them usually disrupt whole sets of segments. The approximately 25 segmentation genes in Drosophila are transcribed after fertilization; so they don’t exhibit a genetic maternal effect, and their expression is regulated by the Bicoid and Nanos protein gradients. The segmentation genes fall into three groups . Gap genes define large sections of the embryo; mutations in these genes eliminate whole groups of adjacent segments. Mutations in the Krüppel gene, for example, cause the absence of several adjacent segments. Pair-rule genes define regional sections of the embryo and affect alternate segments. Mutations in the even-skipped gene cause the deletion of even-numbered segments, whereas mutations in the fushi tarazu gene cause the absence of odd-numbered segments. Segment-polarity genes affect the organization of segments. Mutations in these genes cause part of each segment to be deleted and replaced by a mirror image of part or all of an adjacent segment. For example, mutations in the gooseberry gene cause the posterior half of each segment to be replaced by the anterior half of an adjacent segment. The gap genes, pair-rule genes, and segment-polarity genes act sequentially, affecting progressively smaller regions of the embryo. First, the egg-polarity genes activate or repress the gap genes, which divide the embryo into broad regions. The gap genes, in turn, regulate the pair-rule genes, which affect the development of pairs of segments. Finally, the pairrule genes influence the segment-polarity genes, which guide the development of individual segments.<br /> <br />Homeotic genes:- <br /> After the segmentation genes have established the number and orientation of the segments, homeotic genes become active and determine the identity of individual segments. Eyes normally arise only on the head segment, whereas legs develop only on the thoracic segments. The products of homeotic genes activate other genes that encode these segment-specific characteristics. Mutations in the homeotic genes cause body parts to appear in the wrong segments. Homeotic mutations were first identified in 1894, when William Bateson noticed that floral parts of plants occasionally appeared in the wrong place: he found, for example, flowers in which stamens grew in the normal place of petals. In the late 1940s, Edward Lewis began to study homeotic mutations in Drosophila, which caused bizarre rearrangements of body parts.<br />Homeotic genes create addresses for the cells of particular segments, telling the cells where they are within the regions defined by the segmentation genes. When a homeotic gene is mutated, the address is wrong and cells in the segment develop as though they were somewhere else in the embryo. Homeotic genes are expressed after fertilization and are activated by specific concentrations of the proteins produced by the gap, pair-rule, and segment-polarity genes. The homeotic genes encode regulatory proteins that<br />bind to DNA; each gene contains a subset of nucleotides, called a homeobox, that are similar in all homeotic genes.<br /> The homeobox consists of 180 nucleotides and encodes 60 amino acids that serve as a DNA-binding domain; this domain is related to the helix-turn-helix motif. Homeoboxes are also present in segmentation genes and other genes that play a role in spatial development. There are two major clusters of homeotic genes in Drosophila. One cluster, the Antennapedia complex, affects the development of the adult fly’s head and anterior thoracic segments. The other cluster consists of the bithorax complex and includes genes that influence the adult fly’s posterior thoracic and abdominal segments. Together, the bithorax and Antennapedia genes are termed the homeotic complex (HOM-C). In Drosophila, the bithorax complex contains three genes, and the Antennapedia complex has five; they are all located on the same chromosome. In addition to these eight genes, HOM-C contains many sequences that regulate the homeotic genes.<br /> Remarkably, the order of the genes in the HOM-C is the same as the order in which the genes are expressed along the anterior–posterior axis of the body. The genes that are expressed in the more anterior segments are found at the one end of the complex, whereas those expressed in the more posterior end of the embryo are found at the other end of complex. The reason for this correlation is unknown.<br />Homeobox Genes in Other Organisms:-<br /> After homeotic genes in Drosophila had been isolated and cloned, molecular geneticists set out to determine if similar genes exist in other animals; probes complementary to the homeobox of Drosophila genes were used to search for homologous genes that might play a role in the development of other animals. The search was hugely successful: homeobox-containing (Hox) genes have been found in all<br />animals studied so far, including nematodes, beetles, urchins, frogs, birds, and mammals. They have even been discovered in fungi and plants, indicating that Hox genes arose early in the evolution of eukaryotes.<br />In vertebrates, there are four clusters of Hox genes, each of which contains from 9 to 11 genes. Interestingly, the Hox genes of other organisms exhibit the same relation between order on the chromosome and order of their expression along the anterior–posterior axis of the embryo as that of Drosophila. Mammalian Hox genes, like those in Drosophila, encode transcription factors that help determine the identity of body regions along an anterior– posterior axis.<br />The Control of Development:-<br /> Development is a complex process consisting of numerous events that must take place in a highly specific sequence. The results of studies in fruit flies and other organisms reveal that this process is regulated by a large number of genes. In Drosophila, the dorsal–ventral axis and the anterior–posterior axis are established by maternal genes these genes encode mRNAs and proteins that are localized to specific regions within the egg and cause specific genes to be expressed in different regions of the embryo. The proteins of these genes then stimulate other genes, which in turn stimulate yet other genes in a cascade of control. As might be expected, most of the gene products in the cascade are regulatory proteins, which bind to DNA and activate other genes. In the course of development, successively smaller regions of the embryo are determined .<br />In Drosophila, first, the major axes and regions of the embryo are established by egg polarity genes. Next, patterns within each region are determined by the action of segmentation genes: the gap genes define large sections; the pair-rule genes define regional sections of the embryo and affect alternate segments; and the segment-polarity genes affect individual segments. Finally, the homeotic genes provide each segment with a unique identity. Initial gradients in proteins and mRNA stimulate localized gene expression, which produces more finely located gradients that stimulate even more localized gene expression. Developmental regulation thus becomes more and more narrowly defined. The processes by which limbs, organs, and tissues form (called morphogenesis) are less well understood, although this pattern of generalized-to-localized gene expression is encountered frequently.<br />Programmed Cell Death in Development:-<br /> Cell death is an integral part of multicellular life. Cells in many tissues have a limited life span, and they die and are replaced continually by new cells. Cell death shapes many body parts during development: it is responsible for the disappearance of a tadpole’s tail during metamorphosis and causes the removal of tissue between the digits to produce the human hand. Cell death is also used to eliminate dangerous cells that have escaped normal controls.<br /> Cell death in animals is often initiated by the cell itself in a kind of cellular suicide termed apoptosis. In this process, a cell’s DNA is degraded, its nucleus and cytoplasm shrink, and the cell undergoes phagocytosis by other cells without any leakage of its contents . Cells that are injured, on the other hand, die in a relatively uncontrolled manner called necrosis. In this process, a cell swells and bursts, spilling its contents over neighboring cells and eliciting an inflammatory response. Apoptosis is essential to embryogenesis; most multicellular animals cannot complete development if the process is inhibited. Surprisingly, most cells are programmed to undergo apoptosis and will survive only if the internal death program is continually held in check. The process of apoptosis is highly regulated and depends on numerous signals inside and outside the cell. Geneticists have identified a number of genes having roles in various stages of the regulation of apoptosis. Some of these genes encode enzymes called caspases, which cleave other proteins at specific sites (after aspartic acid). Each caspase is synthesized as a large, inactive precursor that is activated by cleavage, ofterv by another caspase.When one caspase is activated, it cleaves other procaspases that trigger even more caspase activity. The resulting cascade of caspase activity eventually cleaves proteins essential to cell function, such as those supporting the nuclear membrane and cytoskeleton. Caspases also cleave a protein that normally keeps an enzyme that degrades DNA (DNAse) in an inactive form. Cleavage of this protein activates DNAse and leads to the breakdown of cellular DNA, which eventually leads to cell death. Procaspases and other proteins required for cell death are continuously produced by healthy cells, so the potential for cell suicide is always present. A number of different signals can trigger apoptosis; for instance, infection by a virus can activate immune cells to secrete substances onto an infected cell, causing that cell to undergo apoptosis. This process is believed to be a defense mechanism designed to prevent the reproduction and spread of viruses. Similarly, DNA damage can induce apoptosis and thus prevent the replication of mutated sequences. Damage to mitochondria and the accumulation of a misfolded protein in the endoplasmic reticulum also stimulate programmed cell death. <br /> Apoptosis in animal development is still poorly understood but is believed to be controlled through cell–cell signaling. The cell death that causes the disappearance of a tadpole’s tail, for example, is triggered by thyroxin, a hormone produced by the thyroid gland that increases in concentration during metamorphosis. The elimination of cells between developing fingers in humans is thought to result from localized signals from nearby cells. The symptoms of many diseases and disorders are caused by apoptosis or, in some cases, its absence. In neurodegenerative diseases such as Parkinson disease and Alzheimer disease, symptoms are caused by a loss of neurons through apoptosis. In heart attacks and stroke, some cells die through necrosis, but many others undergo apoptosis. Cancer is often stimulated by mutations in genes that regulate apoptosis, leading to a failure of apoptosis that would normally eliminate cancer cells.<br />Evo-Devo: The Study of Evolution and Development:-<br /> “Ontogeny recapitulates phylogeny” is a familiar phrase that was coined in the 1860s by German zoologist Ernst Haeckel to describe his belief—now considered wrong—that organisms repeat their evolutionary history during development. According to Haeckel’s theory, a human embryo passes through fish, amphibian, reptilian, and mammalian stages before developing human traits.<br /> Although ontogeny does not recapitulate phylogeny, many evolutionary biologists today are turning to the study of development for a better understanding of the processes and patterns of evolution. Sometimes called “evo-devo,” the study of evolution through the analysis of development is revealing that the same genes often shape developmental pathways in distantly related organisms. In humans for example, the same gene controls the development of eyes, despite the fact that insect and mammalian eyes are thought to have evolved independently. Similarly, biologists once thought that segmentation in vertebrates<br />and invertebrates was only superficially similar, but we now know that, in both Drosophila and amphioxus (a marine organism closely related to vertebrates). A gene<br />called distalless, which creates the legs of a fruit fly, has also been found to also play a role in the development of crustacean branched appendages. This same gene also stimulates body outgrowths of many other organisms, from polycheate worms to starfish. Similar genes may be part of a developmental pathway<br />common to two different species but have quite different effects. For example, a Hox gene called AbdB helps define the posterior end of a Drosophila embryo; a similar group of genes in birds divides the wing into three segments.<br /> The theme emerging from these studies is that a small, common set of genes may underlie many basic developmental processes in many different organisms. Evo-devo is proving that development can reveal much about the process of evolutions.<br />REFERENCES:-<br />Genetics a conceptual approach by Benjamin Pierce.<br />