The common fruit fly was one of the first organisms used to explore the mechanisms of inheritance. It became a model for the study of transmission genetics. In fact, some of the genetic insights from work with Drosophila are so fundamental that it is easy to take them for granted. But research with model organisms has continued to add dramatically to understanding our own genetics and development. A model organism offers some advantages—a known or small genome, simple develop, or easy rearing for mating studies and identification of mutations. Escherichia coli, yeast, round worms, and even simple plants allow us to see into the common genetic processes that are shared by all forms of life.
Most of the important discoveries that are the foundation of medical genetics could not have been made in humans. Fundamental genetic mechanisms often require large numbers of replications, controlled genotypes and environments, experimental manipulation of the genome or the developmental pathways each controls, and the use of tools like mutagenesis. Even when not outright illegal, these would be far too complex and time-consuming to apply to human families and populations. Thus, to ignore the contributions that model organisms have made to understanding human genetics is very shortsighted. Simple animals allow us to study in depth the many biological processes we share with them, and for those critical insights they deserve our respect.
Some examples of Nobel Prize winning genetic contributions using model organisms are shown in Table 16-1. The work of Thomas Hunt Morgan on basic transmission genetics earned the prize for defining the role of chromosomes in heredity. His experimental organism was Drosophila. Its ease of culture, special developmental characteristics like giant polytene (or endoduplicated) chromosomes, and the collection of mutations affecting all elements of development allowed Drosophila melanogaster to become the experimental model of choice. Using Drosophila, processes like the mutagenic effect of X-rays and the way genes control early embryonic steps in development were discovered. Similarly, the defined number of cells and the strict lineage of cell differentiation in the nematode Caenorhabditis elegans illustrated how science can draw general insights from the special characteristics of a model organism.
Table 16-1.Some Nobel Prizes for Genetic Research Using Model Organisms With General Applicability to Humans |Favorite Table|Download (.pdf) Table 16-1. Some Nobel Prizes for Genetic Research Using Model Organisms With General Applicability to Humans
|Year ||Awardees ||Organism ||Primary Contribution |
|1933 ||T.H. Morgan ||Drosophila melanogaster ||Discoveries concerning the role played by the chromosomes in heredity |
|1946 ||H.J. Muller ||Drosophila melanogaster ||Discovery of the production of mutations by x-ray irradiation |
|1958 ||G.W. Beadle, E.L. Tatum, and J. Lederberg || |
|Discovery that genes act by regulating definite chemical events; Gene organization and recombination in bacteria |
|1965 ||F. Jacob, A. Lwoff, and J. Monod ||Escherichia coli ||Genetic control of enzymes and virus synthesis |
|1983 ||B. McClintock ||Zea mays ||Discovery of mobile genetic elements |
|1995 ||E.B. Lewis, C. Nüsslein-Volhard, and E.F. Wieschaus ||Drosophila melanogaster ||Genetic control of early embryonic development |
|2001 ||L.H. Hartwell, R.T. Hunt, and P.M. Nurse || |
Arbacia (sea urchins)
|Discoveries about key regulators of the cell cycle |
|2002 ||S. Brenner, H.R. Horvitz, and J.E. Sulston ||Caenorhabditis elegans ||Genetic regulation of organ development and programmed cell death |
|2006 ||A.Z. Fire and C.C. Mello ||Caenorhabditis elegans ||Discovery of gene silencing or RNA interference by double-stranded RNA |
|2007 ||M.R. Capecchi, M.J. Evans, and O. Smithies ||Mus musculus ||Introduction of specific gene modifications in mice by embryonic stem and cells |
|2009 ||E.H. Blackburn, C.W. Greider, J.W. Szostak ||Tetrahymena ||Discovery of the way chromosomes are protected by telomeres and and telomerase |
|2012 ||J.B. Gurdon and S. Yamanaka || |
|Discovery that mature cells can become pleuripotent again after programming |
A unifying concept here, indeed in all of biology, is "homology. " This biological term refers to the similarities found in structure or function due to shared derivation from a common ancestor. What we learn from model organisms often has a revolutionary impact on our understanding of our own species. The discovery of transposable elements in maize, chromosomal telomeres in Tetrahymena and yeast, and even the way that the genes in bacteria and molds control biochemical pathways illustrate the importance of model organisms. It is a significant theme, because it typifies the direction that biomedical research must continue to take for the future.
Model organisms are exactly that—they are models. But models are only useful to the extent that they give an insight into general processes or to the mechanisms at work in a system of prime interest, like human biology and development. Model organisms like Drosophila, C. elegans, and the others help us understand the general rules of genetic regulation that remind us about the continuity of life. When T.H. Morgan first began to study gene organization on Drosophila chromosomes, he could have had no idea that a discovery like the homeobox genes, which specify key elements of body organization in Drosophila, would open new avenues to understanding the developmental architecture of all organisms. Indeed, the so-called "bottom line" is that experimental research on model organisms will continue to be critically important for future advances in human genetics, because we share with all organisms a major part of our biological heritage.
The Common Fruit Fly, Drosophila melanogaster—Historical Contributions and its Continuing Importance as a Genetic Model
A landmark in the history of genetics was the discovery of a white-eyed mutation in a culture of Drosophila being used by T.H. Morgan to study population growth dynamics. This event began a long history in which Drosophila has been used to explore many fundamental mechanisms of genetics. Genetic research is now stimulated by the extensive mutation collections of resource centers and the experimental innovation of Drosophila researchers. The creativity of researchers keeps opening new horizons. Of course, all of this would be essentially irrelevant were it not for the fundamental genetic similarity that Drosophila shares with all other species.
T.H. Morgan was awarded the Nobel Prize in 1933 for his work on the patterns of genetic transmission by chromosomes. The Nobel Prize can only be awarded to a living scientist, so Gregor Mendel was not eligible. But insights from Mendel, Morgan, and Morgan's students including the later Nobel Laureate H.J. Muller, established the foundation for understanding mechanisms of gene transmission, linkage and sex-linkage, recombination, and changes in chromosome structure. Drosophila offers many experimental advantages. One is that the chromosomes of the Drosophila larval salivary glands undergo DNA replication for many cycles without cell division, creating giant chromosomes having about 1000 matched copies of the DNA strand lying together in a cable that shows significant chromosome detail. This makes it possible to map specific gene functions to specific physical regions of a chromosome, and changes in chromosome structure can be mapped precisely.
This would be an interesting historical footnote if the story stopped there. But it did not. In the years since then, Drosophila has become one of the most important experimental organisms for exploring the role of genes in development, physiology, and behavior.
In part this is because many gene and special chromosome mutations have been identified over the years. These allow experiments to target processes that are difficult to match in other organisms. It also made it possible to apply the techniques of recombinant DNA when they first became available, and the discoveries from that work identified genetic mechanisms that were found to be in common with other organisms.
Drosophila has a genome of about 13,600 genes. About a quarter of its genome is made up of highly-repetitive DNA and several dozen kinds of transposable elements. Some of the earliest work on transposable elements, the P-elements of "mutator activity" or "hybrid dysgenesis," was done with Drosophila. P-elements have now become a powerful experimental tool for targeted mutagenesis and other genome manipulations.
At the other end of the phenotypic spectrum, research using Drosophila explored the genetic basis of quantitative traits. These are traits that vary in expression because the effect of each gene can be enhanced or masked by environmental factors affecting the same trait. Using carefully controlled experiments that factored out environmental effects, experiments with Drosophila showed that even apparently complex expression could often be explained by genetic variation in a relatively small number of contributing genes. This perspective should change a physician's approach to complex traits. Although variable in presentation, a condition may still be traced to a predictable biological process.
The International Commission on Zoological Nomenclature has moved to change the taxonomic name of this genetic landmark organism to Sophophora melanogaster. It is a change that may be justified taxonomically but is criticized by the genetic research community. This may be a rare example of consistency and stability of the literature being more important to the growth of science than is taxonomic precision. It is a change that is likely to be ignored by most geneticists for a long time. But do not be confused if you find this name in your future journal reading.
A Bacterium, Escherichia coli
Escherichia coli is one of the most important model systems for understanding simple genome organization and is central to areas like recombinant DNA technology development. On the other hand, some strains of E coli cause food-borne illness that can be quite serious. As a species, its genome is exceeding diverse, but the strains, like E coli K12, used in microbial genetics are restricted in number. A representative genome was first reported in 1997. It is a circular DNA molecule of 4.6 million base pairs with 4288 protein-coding genes, 7 rRNA genes, and 86 tRNA genes. But the number of genes varies among strains, and some genes may have come from horizontal transfer from other organisms. These variables add to the utility of E coli as an experimental organism for genetic study.
Joshua Lederberg and Edward Tatum discovered the process of bacterial conjugation in E coli, and Seymour Benzer utilized E coli and the T4 bacteriophage to study the linearity of gene structure in the genome. A foundation of modern biotechnology can be traced to work with plasmids and restriction enzymes in E coli. One early application of recombinant DNA technology was the production of human insulin from E coli.
Baker's Yeast, Saccharomyces cerevisiae
Yeast is a developmentally simple eukaryote, with a life cycle that has both haploid and diploid phases. Its short generation time allows experiments to be carried out efficiently using techniques, like plating colonies on petri dish media, that parallel some of those available for bacteria. In addition to employing mutations to dissect components of a developmental process, Saccharomyces is being used to study signal transduction pathways that alter cell phenotypes.
Although the Saccharomyces genome was completely sequenced by 1996, geneticists are still uncertain how many functional genes are present in its genome. It is likely that the number is about 6000 or so, but many hypothetical genes have functions that are not yet known. In addition to protein-coding genes, there are many noncoding RNAs, including 274 tRNA genes and RNAs for ribosome processing, intron splicing, and other cellular processes. About 20% of the loci lead to lethality when mutated. Recombination rates are higher than those for most other fungi, and good genetic maps are available for a large number of loci.
The proportion of repeated sequences is much lower than that found in most multicellular eukaryotes (see Chapter 4). About 4% of the Saccharomyces cerevisiae genome is composed of transposable elements. The virus-like retroelement Ty is found in about 50 copies in each genome. Intact Ty elements can pair and recombine even when they are located on different chromosomes, resulting in frequent reciprocal translocations and other chromosomal aberrations.
There are two mating types, a and α. Signal transduction pathways can be activated by pheromones that are released by cells of one mating type and then bind to receptors on the other mating type. This activates an intracellular cascade that phosphorylates, and thus activates, a transcription factor. This in turn activates the genes needed for arresting the G1 cell cycle and for cell fusion and nuclear fusion required for mating. This type of signal transduction pathway studied in yeast is highly conserved in eukaryotes.
A Nematode, Caenorhabditis elegans
The nematode Caenorhabditis elegans is a simple eukaryote with precisely 959 cells in a female, which is a functional hermaphrodite, and 1031 cells in a male. The cell lineage relationships in both sexes are now completely mapped (Figure 3-12). Six founder cells give rise to all the cells of the adult, and mutations that alter cell lineage progression are a valuable tool for developmental analysis. Adults are about 1 mm long and can be handled with techniques that resemble those used to culture bacterial cell colonies. Since it is transparent, mutations affecting its internal anatomy and development can be studied easily. Each mating can yield hundreds of progeny, and it shares many of the experimental advantages that have benefited work with Drosophila. The sequence of its approximately 14,000 gene genome was completed in 1998. Insights into genetic control of development using Caenorhabditis elegans were recognized by the Nobel Prize to Sydney Brenner, Robert Horvitz, and John Sulston in 2002.
One special benefit of C elegans as an experimental model is the fact that its cell lineage during normal development is strictly defined (see Figure 3-12). The specific fate of each progenitor cell has been mapped. With this map it has been possible to define inductive signals between one cell and another, the signal transduction pathways of the recipient cell, and genetically programmed cell death events. Gene expression in C elegans has some unexpected elements, such as examples of polycistronic transcription like that seen in bacteria. One process discovered in C elegans is RNA-mediated interference (RNAi). When used as an experimental technique, it allows researchers to study the function of targeted genes by silencing their expression.
The Zebrafish, Danio rerio
The zebrafish, Danio rerio, shares many characteristics with other model genetic systems. They have a short generation time and they lay several hundred eggs in each reproductive cycle. An important advantage for researchers is that the embryos are relatively large and transparent. This means that internal developmental changes can be observed easily. The precursors to major organs become visible through the body wall within about 36 hours after fertilization, and hatching occurs up to about 36 hours later. The genome of D rerio has been sequenced and many genetically-characterized strains are available to researchers. Among these are strains that allow study of diurnal sleep cycles, which are similar to those of mammals.
Using anti-sense technologies, important aspects of development can be studied. This technique uses Morpholino oligonucleotides. These synthetic nucleotide chains of RNA or DNA bind to complementary sequences when injected into an embryo. By binding to a complementary sequence in a cell, they effectively inactivate it and, thus, mimic a mutation. This reduces gene expression in the cell and its descendants. The technique allows the equivalent of targeted mutagenesis to explore genetic effects on development of a vertebrate with many homologies to human biology.
The House Mouse, Mus musculus
As a mammal that shares many aspects of physiology and development with humans, it is not surprising that our genomes are similar in size (about 3 billion bp) and content. In fact, extended regions of gene sequence similarity have been identified showing that even the organization of our genomes retains extensive homology. Gene sequence similarities are also reflected in functional parallels. Thus, homology makes the house mouse an especially valuable model for understanding human genetics. Advanced cellular and molecular techniques can be combined readily with more traditional genetic mating systems. One specific example is the use of Mus to develop models of many human genetic diseases.
As an experimental model, they benefit from a relative short life cycle (8 or 9 weeks), small body size, and comparatively large litters of offspring. Transgenic manipulation allows complex processes to be isolated and studied. With nuclear injection, one can add specific genes to the genome. Targeted mutagenesis can change or inactivate a locus of choice. In contrast to the defined cell lineage outcomes associated with cells of C elegans, cells in the early embryonic stages of Mus retain totipotency, or developmental flexibility. It is therefore possible to generate chimeras, composed of cells derived from two or more separate genotypes. Literally hundreds of single-gene mutations are now available in strains with well-documented genetic backgrounds, providing a rich resource for advanced experimental design. Among these are the Hox genes, homologous to the homeobox genes first described in Drosophila, which define critical elements of body plan in all multicellular organisms (Figures 13-19 and 13-20).
A Model Plant, Arabidopsis thaliana
Arabidopsis thaliana (Figure 16-1) is a small weed with no special economic importance, other than being a model plant for genetic studies. Its small size, five pairs of well-banded chromosomes, and relatively tiny genome offer an ideal organism in which to study the molecular biology and genetic control of processes like growth, biochemical pathways, and development of a plant. Its genome was published in 2000. Transposable elements that had originally been identified in corn can be introduced into A thaliana cells and become integrated into its genome. Agrobacterium is the biological agent both for this process and for transformation by plasmid DNA called T-DNA. Insertional mutagenesis is a powerful technique for generating mutations to study biochemical and developmental processes.
Arabidopsis thaliana, a model plant. This plant has no true agricultural or ecosystem value. Its importance exists in its role as a research organism. (© Jeremy Burgess/Photo Researchers.)
Genetic analysis has yielded insights into the control of development by plant hormones and in response to light, a complex of processes known as photomorphogenesis. Although plants do not contain a homeobox like that in animals, they have a functionally equivalent group of genes that code for DNA-binding transcription factors. Surprisingly, a degree of partial homology between this plant's steroid-like gene and mammalian genes of the steroid pathway suggests that future research may uncover even more fundamental genetic connections among distantly-related organisms.
What Does This Reveal About Human Disease?
Comparative genomics hybridization is the discipline of studying genetic relationships across species. While information can be obtained in one species and applied to another, translating that information into practical applications is much more difficult. First, animal physiology is not an exact replica of that in humans. Caution has to be taken before a treatment in a model organism is verified in humans. Second, even though a particular gene may be homologous by sequence between two organisms, it is not necessarily true that the gene will perform the same function in each nor will phenotypes be predictable. For example, mutations in the eya gene produce a phenotype in Drosophila that is "eyes absent." But mutations in the homologous human gene EYA1 produces a phenotype of branchio-oto-renal syndrome—a condition associated with malformations of the branchial arch structures, kidneys, and ears/hearing. This then is a double-edged sword. While caution has the be taken in making any projections or extrapolations, it is impressive to consider that studies of the veins in fruit fly wings can give critical insights into processes like cancer, stress responses, and neural networks!
Table 16-2 lists several other such known relationships. We will describe just a few of these in more detail. Saethre-Chotzen syndrome is a disorder characterized by craniosynostosis and other craniofacial anomalies as well as digital changes (Figure 16-2 b, c). It is caused by a mutation in a gene known as TWIST which is a transcriptional regulator. The Drosophila homolog gene is designated twist. Mutations in this gene in Drosophila produce segmentation defects of myogenesis (Figure 16-2 a). The hedgehog gene in Drosophila gets its name from a mutation that produces short bristly hairs on the larvae that are reminiscent of a hedgehog (Figure 16-3a). The human homolog has been termed Sonic hedgehog (SHH). Mutations in SHH have been shown to cause heritable non-syndromic holoprosencephaly (Figures 16-3 b, c, d). The phenotypic spectrum of SHH in humans may be as mild as only showing a single central incisor (Figure 16-3 e).
Table 16-2.Examples of Different Phenotypes Associated with Homologous Genes Across Species |Favorite Table|Download (.pdf) Table 16-2. Examples of Different Phenotypes Associated with Homologous Genes Across Species
|Drosophila Gene ||Drosophila Phenotype ||Mouse Gene ||Mouse Phenotype ||Human Gene ||Human Disease ||Human Signs/Symptoms |
|paired ||Failure of posterior segment development ||Splotch (Sp) ||Neural tube defects ||PAX3 ||Waardenburg syndrome ||Hearing loss, pigmentation defects, congenital anomalies |
|cubitus interruptus ||Abnormal wing formation ||Gli ||Failure to thrive, early death, Hirschprung ||GLI1 ||Glioblastoma oncogene ||Brain tumors |
| || ||Gli2 || || || || |
| || ||Gli3 ||Malformations of GI, respiratory, renal and skeletal systems ||GLI3 ||Greig cephalosyndactyly, Pallister Hall syndrome ||Polysyndactyly, craniosynostosis, brain hamartomas |
|hedgehog ||Larva with short curly hairs ||Shh ||Ventral induction defects, abnormal somites, vertebral and rib anomalies ||SHH (Sonic hedgehog) ||Holoprosencephaly ||Non-syndromic holoprosencephaly |
| || ||Ihh ||Bony defects due to abnormal chondrocyte differentiation ||IHH (Indian hedgehog) ||Brachydactyly ||Shortened fingers |
|patched ||Abnormal wing formation ||Ptc ||Hindlimb defects, brain tumors ||PTCH1 ||Gorlin (basal cell nevus) syndrome ||Basal cell tumors, jaw cysts, rib anomalies |
|twist ||Abnormal myogenesis ||Twist ||Neural tube, limb and somite anomalies ||TWIST ||Saethre Chotzen syndrome ||Asymmetric craniofacial anomalies, digital anomalies |
|eyes absent ||Absent eyes ||Eya1 ||Missing ears and kidneys, abnormal apoptosis of organ primordia ||EYA1 ||Branchio-oto-renal syndrome ||Branchial arch defects, ear anomalies/deafness, renal malformations |
|engrailed ||Abnormal development of imaginal discs ||En2 ||Frequently lethal, cerebellar anomalies ||EN2 ||Autism susceptibility ||Autism |
(a) Drosophila larva with abnormal myogenesis due to twist mutation. (b) Craniofacial changes in a young girl with Saethre Chotzen with a known TWIST gene mutation. (c) Broad great toe in same patient. (a: Reprinted with permission from Castanon I, Von Stetina S, Kass J, et al. Dimerization partners determine the activity of the Twist bHLH protein during Drosophila mesoderm development. Development 2001 128:3145-3159.)
(a) Normal Drosophila larva on left. The larva on the right has a mutation in the hedgehog gene. (b) Patient with holoprosencephaly with severe bilateral cleft lip and palate. He has a positive family history with 2 half-brothers also affected. (c,d) Brain MRI of the boy in frame b showing incomplete ventral induction (separation of midline)—semi-lobar holoprosencephaly. (e) Their mother has a minor expression of the condition as a single central incisor. She and all 3 boys have an SHH mutation. (a: Reprinted with permission from van den Brink GR. Hedgehog Signaling in Development and Homeostasis of the Gastrointestinal Tract Physiol Rev October 2007 87:(4) 1343-1375; doi:10.1152/physrev.00054.2006.)
Basal cell nevus syndrome (previously called Gorlin syndrome) is associated with craniofacial dysmorphisms, jaw cysts, palmar and plantar pits, and the propensity to develop basal cell carcinomas (Figure 16-4b, c, d). It is caused by a gene called PTCH1. The Drosophila homolog is the patched gene. Mutations in this gene cause a variety of fly wing anomalies (Figure 16-4a). One last example is that of Splotch mutations in mice which produce defects in neural tube development (Figure 16-5 a). The human homolog is the homeobox gene PAX3. PAX3 mutations are seen in some patients with Waardenburg syndrome, although there is genetic heterogeneity for this condition. Waardenburg syndrome is characterized by neurosensory hearing loss and telecanthus (lateral displacement of the inner canthi of the eyes). Patients with Waardenburg syndrome also will have a variety of pigmentary changes including a characteristic "white forelock" of hair, iris heterochromia, and poliosis (patchy hypopigmentation of the hair and skin). These features are shown in Figure 16-5(b-d).
(a) Multiple wing malformations associated with patched mutation. (b) Adolescent girl with Gorlin (basal cell nevus) syndrome. She has a confirmed PTC mutation. Patients with Gorlin syndrome are reported to have broad facies, frontal bossing and prominent jaws. (c) Basal cell tumors on the foot. (d) Palmar pits. (e) Head CT scan demonstrating odontogenic keratocysts (in the jaw). (a: Reprinted with permission from Johnson RL, Milenkovic L, Scott MP. In Vivo Functions of the Patched Protein: Requirement of the C Terminus for Target Gene Inactivation but Not Hedgehog Sequestration, Molecular Cell, volume 6, issue 2, August 2000, pp 467-478, ISSN 1097-2765, 10.1016/S1097-2765 (00)00045-9.)
(a) Mice embryos. The one on the left is normal. The one on the right has a Splotch mutation and is showing defects of neural tube development. (b) Young girl with Waardenburg syndrome. She presented with neurosensory hearing loss. She has a known PAX 3 mutation. (Note white hair patch and dystopia canthorum). (c) Hypopigmented area of skin on her leg. (d) Young boy with Waardenburg syndrome. Note iris heterochromia. (a: Reprinted with permission from Conway SJ, Henderson DJ, Kirby ML, et al. Development of a lethal congenital heart defect in the splotch (Pax3) mutant mouse Cardiovasc Res (1997) 36(2): 163-173 doi:10.1016/S0008-6363(97)00172-7.)