The Genetic Basis of Development

I.         In the development of most multicellular organisms, a single-celled zygote gives rise to cells of many different types.

            A.        Each type has a different structure and corresponding function.

            B.        Cells of similar types are organized into tissues, tissues into organs, organs into organ systems, and organ systems into the whole organism.

            C.        Thus, the process of embryonic development must give rise not only to cells of different types, but also to higher-level structures arranged in a particular way in three dimensions.

II.        Embryonic development involves cell division, cell differentiation, and morphogenesis.

            A.        An organism arises from a fertilized egg cell as the result of three interrelated processes: cell division, cell differentiation, and morphogenesis.

            B.        Through a succession of mitotic cell divisions, the zygote gives rise to a large number of cells.

                        1.         Cell division alone would produce only a great ball of identical cells.

                                    a.         During development, cells become specialized in structure and function, undergoing cell differentiation.

                                    b.         Different kinds of cells are organized into tissues and organs.

                                    c.         The physical processes that give an organism its shape constitute morphogenesis.

            C.        Early events of morphogenesis lay out the basic body plan very early in embryonic development.

                        1.         These include establishing the head of an animal embryo or the roots of a plant embryo.

                        2.         Later morphogenetic events establish relative locations within smaller regions of the embryo, such as the digits on a vertebrate limb.

            D.        The overall schemes of morphogenesis in animals and plants are very different.

                        1.         In animals, but not in plants, movements of cells and tissues are necessary to transform the embryo into the characteristic 3-D form of the organism.

                        2.         In plants, morphogenesis and growth in overall size are not limited to embryonic and juvenile periods but occur throughout the life of the plant.

III.       Cell differentiation results from differential gene expression.

            A.        During differentiation and morphogenesis, embryonic cells behave and function in ways different from one another, even though all of them have arisen from the same zygote.

            B.        The differences between cells in a multicellular organism come almost entirely from differences in gene expression, not differences in the cell’s genomes.

            C.        These differences arise during development, as regulatory mechanisms turn specific genes off and on.

            D.        An important question that emerges is whether genes are irreversibly inactivated during differentiation.

                        1.         The fact that a mature plant cell can dedifferentiate (reverse its function) and give rise to all the different kinds of specialized cells of a new plant shows that differentiation does not necessarily involve irreversible changes in the DNA.

                                    a.         In plants, at least, cells can remain totipotent. They retain the zygote’s potential to form all parts of the mature organism.

                        2.         Differentiated cells from animals often fail to divide in culture, much less develop into a new organism.

                                    a.         Animal researchers have approached the question by replacing the nucleus of an unfertilized egg or zygote with the nucleus of a differentiated cell.

                                    b.         The ability of the transplanted nucleus to support normal development is inversely related to the donor’s age.

                                                (1)       Transplanted nuclei from relatively undifferentiated cells from an early embryo lead to the development of most eggs into tadpoles.

                                                (2)       Transplanted nuclei from fully differentiated intestinal cells lead to fewer than 2% of the cells developing into normal tadpoles.

                                    c.         Most of the embryos failed to make it through even the earliest stages of development.

            E.        Developmental biologists agree on several conclusions about these results.

                        1.         First, nuclei do change in some ways as cells differentiate. While the DNA sequences do not change, histones may be modified or DNA may be methylated.

                        2.         In most animals, nuclear “potency” tends to be restricted more and more as embryonic development and cell differentiation progress.

                        3.         In the nuclei of fully differentiated cells, a small subset of genes is turned on and the expression of the rest is repressed.

                                    a.         This regulation is often the result of changes in chromatin, such as the acetylation of histones or the methylation of DNA.

                                    b.         Many of these changes must be reversed in the nucleus of the donor animal in order for genes to be expressed or repressed appropriately for early stages of development.

                                    c.         Researchers have found that the DNA in embryonic cells from cloned embryos, like that of differentiated cells, often has more methyl groups than does the DNA in equivalent cells from uncloned embryos of the same species.

                                    d.         Because DNA methylation helps regulate gene expression, methylated DNA of donor nuclei may interfere with the pattern of gene expression necessary for normal embryonic development.

            F.        Another hot research area involves stem cells, a cell that is relatively unspecialized, can reproduce itself and, under appropriate conditions, differentiate into specialized cell types.

                        1.         The ultimate goal of stem cell research is to supply cells for the repair of damaged or diseased organs.

                        2.         Many early animal embryos contain totipotent stem cells, which can give rise to differentiated cells of any type.

                                    a.         In culture, these embryonic stem cells reproduce indefinitely and can differentiate into various specialized cells.

                        3.         The adult body has various kinds of stem cells, which replace nonreproducing specialized cells.

                                    a.         Adult stem cells are said to be pluripotent, able to give rise to many, but not all, cell types.

IV.      Different cell types make different proteins, usually as a result of transcriptional regulation.

            A.        During embryonic development, cells become visibly different in structure and function as they differentiate.

                        1.         The earliest changes that set a cell on a path to specialization show up only at the molecular level.

                        2.         Molecular changes in the embryo drive the process, termed determination, which leads up to observable differentiation of a cell.

                        3.         At the end of this process, an embryonic cell is irreversibly committed to its final fate.

                        4.         If a determined cell is experimentally placed in another location in the embryo, it will differentiate as if it were in its original position.

                        5.         The outcome of determination—cell differentiation—is caused by the expression of genes that encode tissue-specific proteins.

                        6.         These give a cell its characteristic structure and function.

            B.        Differentiation begins with the appearance of mRNA and is finally observable in the microscope as changes in cellular structure.

                        1.         In most cases, the pattern of gene expression in a differentiated cell is controlled at the level of transcription.

                        2.         Cells produce the proteins that allow them to carry out their specialized roles in the organism.

            C.        We believe that certain cell-specific regulatory genes are active in stem cells, leading to specific cell determination.

V.        Transcriptional regulation is directed by maternal molecules in the cytoplasm and signals from other cells.

            A.        Two sources of information “tell” a cell which genes to express at any given time.

                        1.         One source of information is the cytoplasm of the unfertilized egg cell, which contains RNA and protein molecules encoded by the mother’s DNA. Messenger RNA, proteins, other substances, and organelles are distributed unevenly in the unfertilized egg.

                                    a.         Maternal substances that influence the course of early development are called cytoplasmic determinants.

                                                (1)       These substances regulate the expression of genes that affect the developmental fate of the cell.

                                                (2)       After fertilization, the cell nuclei resulting from mitotic division of the zygote are exposed to different cytoplasmic environments.

                                                (3)       The set of cytoplasmic determinants a particular cell receives helps determine its developmental fate by regulating expression of the cell’s genes during the course of cell differentiation.

                        2.         The other important source of developmental information is the environment around the cell, especially signals impinging on an embryonic cell from other nearby embryonic cells.

                                    a.         In animals, these include contact with cell-surface molecules on neighboring cells and the binding of growth factors secreted by neighboring cells.

                                    b.         In plants, the cell-cell junctions known as plasmodesmata allow signal molecules to pass from one cell to another.

                                    c.         The synthesis of these signals is controlled by the embryo’s own genes.

                                    d.         These signal molecules cause induction, triggering observable cellular changes by causing a change in gene expression in the target cell.

VI.      Before morphogenesis can shape an animal or plant, the organism’s body plan must be established.

            A.        Cytoplasmic determinants and inductive signals contribute to pattern formation, the development of spatial organization in which the tissues and organs of an organism are all in their characteristic places.

            B.        Pattern formation begins in the early embryo, when the major axes of an animal and the root-shoot axis of the plant are established.

                        1.         The molecular cues that control pattern formation, positional information, tell a cell its location relative to the body axes and to neighboring cells.

                        2.         They also determine how the cells and their progeny will respond to future molecular signals.

            C.        Gradients of maternal molecules in the early embryo control axis formation.

                        1.         Substances are produced under the direction of maternal effect genes that are deposited in the unfertilized egg.

                                    a.         When a maternal effect gene is mutated, the offspring has an abnormal mutant phenotype.

                                    b.         In fruit fly development, maternal effect genes encode proteins or mRNA that are placed in the egg while it is still in the ovary.

                        2.         When the mother has a mutated gene, she makes a defective gene product (or none at all), and her eggs will not develop properly when fertilized.

                                    a.         These maternal effect genes are also called egg-polarity genes, because they control the orientation of the egg and consequently the fly.

                        3.         One group of genes sets up the anterior-posterior axis, while a second group establishes the dorsal-ventral axis.

                                    a.         One of these, the bicoid gene, affects the front half of the body.

                                    b.         An embryo whose mother has a mutant bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends.

                                    c.         This suggests that the gene’s products are concentrated at the future anterior end.

                                                (1)       This is a specific version of a general gradient hypothesis, in which gradients of morphogens establish an embryo’s axes and other features.

                                                (2)       After the egg is fertilized, bicoid mRNA is transcribed into bicoid protein, which diffuses from the anterior end toward the posterior, resulting in a gradient of proteins in the early embryo.

                                                (3)       Injections of pure bicoid mRNA into various regions of early embryos results in the formation of anterior structures at the injection sites as the mRNA is translated into protein.

                                    d.         Gradients of specific proteins determine the posterior end as well as the anterior and also are responsible for establishing the dorsal-ventral axis.

            D.        A cascade of gene activations sets up the segmentation pattern in Drosophila. The bicoid protein and other morphogens are transcription factors that regulate the activity of some of the embryo’s own genes.

                        1.         Gradients of these morphogens bring about regional differences in the expression of segmentation genes, the genes that direct the actual formation of segments after the embryo’s major axes are defined.

                        2.         In a cascade of gene activations, sequential activation of three sets of segmentation genes provides the positional information for increasingly fine details of the body plan.

                        3.         The three sets are called gap genes, pair-rule genes, and segment polarity genes.

                                    a.         The products of many segmentation genes are transcription factors that directly activate the next set of genes in the hierarchical scheme of pattern formation.

                                    b.         Some are components of cell-signaling pathways, including signal molecules used in cell-cell communication and the membrane receptors that recognize them.

                        4.         Working together, the products of egg-polarity genes such as bicoid regulate the regional expression of gap genes, which control the localized expression of pair-rule genes, which in turn activate specific segment polarity genes in different parts of each segment.

            E.        Homeotic genes direct the identity of body parts.

                        1.         In a normal fly, structures such as antennae, legs, and wings develop on the appropriate segments. The anatomical identity of the segments is controlled by master regulatory genes, the homeotic genes.

                        2.         Mutations to homeotic genes produce flies with such strange traits as legs growing from the head in place of antennae. Structures characteristic of a particular part of the animal arise in the wrong place.

                        3.         Like other developmental genes, the homeotic genes encode transcription factors that control the expression of genes responsible for specific anatomical structures.

                        4.         Scientists are now working to identify the genes activated by the homeotic proteins—the genes specifying the proteins that actually build the fly structures.

            F.        Amazingly, many of the molecules and mechanisms that regulate development in the Drosophila embryo have close counterparts throughout the animal kingdom.

VII.     The development of a multicellular organism requires close communication among cells in the form of cell signaling and induction.

            A.        Once an embryo is truly multicellular, cells signal nearby cells to change in a specific way, in a process called induction.

            B.        Induction brings about cell differentiation through transcriptional regulation of specific genes.

            C.        The nematode C. elegans has proved to be a very useful model organism for investigating the roles of cell signaling, induction, and programmed cell death in development.

                        1.         Researchers know the entire ancestry of every cell in the body of an adult C. elegans—the organism’s complete cell lineage.

                        2.         The pathway from fertilized egg to adult nematode involves four larval stages (during which the larvae look much like smaller versions of the adult) during which this structure develops.

                        3.         Already present on the ventral surface of the second-stage larva are six cells from which the vulva (through which the worm lays its eggs) will arise.

                        4.         A single cell in the embryonic gonad, the anchor cell, initiates a cascade of signals that establishes the fate of the six vulval precursor cells.

                        5.         If an experimenter destroys the anchor cell with a laser beam, the vulva fails to form and the precursor cells simply become part of the worm’s epidermis.

                        6.         Secreted factors or cell-surface proteins bind to receptors on the recipient cell, initiating intracellular signal transduction pathways.

            D.        We can conclude that:

                        1.         In the developing embryo, sequential inductions drive organ formation.

                        2.         The effect of an inducer can depend on its concentration.

                        3.         Inducers produce their effects via signal transduction pathways similar to those operating in adult cells.

                        4.         The induced cell’s response is often the activation of genes—transcriptional regulation—that, in turn, establishes a pattern of gene activity characteristic of a particular kind of differentiated cell.

            E.        Programmed cell death, or apoptosis. is also necessary during development

                        1.         At precise points in development, signals trigger the activation of a cascade of “suicide” proteins in the cells destined to die.

                        2.         During apoptosis, a cell shrinks and becomes lobed (called “blebbing”), the nucleus condenses, and the DNA is fragmented.

                        3.         Neighboring cells quickly engulf and digest the membrane-bound remains, leaving no trace.

                                    a.         In C. elegans, a protein in the outer mitochondrial membrane called Ced-9 (the product of ced-9) is a master regulator of apoptosis.

                                    b.         ced-9 acts as a brake in the absence of a signal promoting apoptosis.

                                    c.         When the cell receives an external death signal, Ced-9 is inactivated, allowing both Ced-4 and Ced-3 to be active.

                                    d.         The apoptosis pathway activates proteases and nucleases to cut up the proteins and DNA of the cell.

                        4.         Apoptosis is regulated not at the level of transcription or translation, but through changes in the activity of proteins that are continually present in the cell.

                                    a.         Apoptosis pathways in humans and other mammals are more complicated, although research on mammals has revealed a prominent role for mitochondria in apoptosis.

                                    b.         Signals from apoptosis pathways or others somehow cause the outer mitochondrial membrane to leak, releasing proteins that promote apoptosis.

                                    c.         Surprisingly, these proteins include cytochrome c, which functions in mitochondrial electron transport in healthy cells but acts as a cell death factor when released from mitochondria.

                        5.         Damaged cells normally generate internal signals that trigger apoptosis.

VIII.    Homeobox genes have been highly conserved in evolution.

            A.        Biologists are finding that the genomes of related species with strikingly different forms may have only minor differences in gene sequence or regulation.

            B.        All homeotic genes of Drosophila include a 180-nucleotide sequence called the homeobox, which specifies a 60-amino-acid homeodomain.

            C.        An identical, or very similar, sequence of nucleotides (often called Hox genes) is found in many other animals, including humans.

            D.        The vertebrate genes homologous to the homeotic genes of fruit flies have even kept their chromosomal arrangement.

            E.        Related sequences have been found in the regulatory genes of plants, yeasts, and even prokaryotes.

                        1.         The homeobox DNA sequence must have evolved very early in the history of life and is sufficiently valuable that it has been conserved virtually unchanged in animals and plants for hundreds of millions of years.

            F.        The homeobox-encoded homeodomain is part of a protein that binds to DNA when the protein functions as a transcriptional regulator.

                        1.         However, the shape of the homeodomain allows it to bind to any DNA segment.

                        2.         Other, more variable, domains of the overall protein determine which genes it will regulate.

                        3.         Interaction of these latter domains with still other transcription factors helps a homeodomain-protein recognize specific enhancers in the DNA.

            G.        Proteins with homeodomains probably regulate development by coordinating the transcription of groups of developmental genes.

            H.        In Drosophila, different combinations of homeobox genes are active in different parts of the embryo and at different times, leading to pattern formation.

            I.         Many other genes involved in development are highly conserved from species to species.

                        1.         These include numerous genes encoding components of signaling pathways.

                        2.         How can the same genes be involved in the development of so many different animals?

                                    a.         In some cases, small changes in regulatory sequences of particular genes can lead to major changes in body form.

                                                (1)       For example, varying expression of the Hox genes along the body axis produce different numbers of leg-bearing segments in insects and crustaceans.

                                                (2)       Plants also have homeobox-containing genes, however, they do not appear to function as master regulatory switches in plants. Other genes appear to be responsible for pattern formation in plants.

IX.      There are some basic similarities—and many differences—in the development of plants and animals.

            A.        The last common ancestor of plants and animals was a single-celled microbe living hundreds of millions of years ago, so the processes of development evolved independently in the two lineages.

                        1.         Plants have rigid cell walls that prevent cell movement, while morphogenetic movements are very important in animals.

            B.        Morphogenesis in plants is dependent on differing planes of cell division and selective cell enlargement.

            C.        Nevertheless, there are some basic similarities of development.

                        1.         In both plants and animals, development relies on a cascade of transcriptional regulators turning on or off genes in a finely tuned series.

            D.        The genes that direct these processes are very different in plants and animals.

                        1.         Quite a few of the master regulatory switches in animals are homeobox-containing Hox genes while those in plants are belong to the Mads-box family of genes.

                        2.         Although homeobox-containing genes can be found in plants and Mads-box genes can be found in animals, they do not play the same major roles in development in plants and animals.

                        3.         The unity of life is reflected in the similarity of biological mechanisms used to establish body pattern, although the exact genes directing develop may differ.

                        4.         The similarities reflect the common ancestry of life on Earth, while the differences have created the diversity of living organisms.