The evolution of present-day cells from a common ancestor has important implications for cell and molecular biology as an experimental science. Because the fundamental properties of all cells have been conserved during evolution, the basic principles learned from experiments performed with one type of cell are generally applicable to other cells. On the other hand, because of the diversity of present-day cells, many kinds of experiments can be more readily undertaken with one type of cell than with another. Several different kinds of cells and organisms are commonly used as experimental models to study various aspects of cell and molecular biology. The features of some of these cells that make them particularly advantageous as experimental models are discussed in the sections that follow.
Because of their comparative simplicity, prokaryotic cells (bacteria) are ideal models for studying many fundamental aspects of biochemistry and molecular biology. The most thoroughly studied species of bacteria is E. coli, which has long been the favored organism for investigation of the basic mechanisms of molecular genetics. Most of our present concepts of molecular biology-including our understanding of DNA replication, the genetic code, gene expression, and protein synthesis-derive from studies of this humble bacterium.
E. coli has been especially useful to molecular biologists because of both its relative simplicity and the ease with which it can be propagated and studied in the laboratory. The genome of E. coli, for example, consists of approximately 4.6 million base pairs and encodes about 4000 different proteins. The human genome is nearly a thousand times more complex (approximately 3 billion base pairs) and encodes about 100,000 different proteins (see Table 1.2). The small size of the E. coli genome provides obvious advantages for genetic analysis, and the sequence of the entire E. coli genome has been determined.
Molecular genetic experiments are further facilitated by the rapid growth of E. coli under well-defined laboratory conditions. Depending on the culture conditions, E. coli divide every 20 to 60 minutes. Moreover, a clonal population of E. coli, in which all cells are derived by division of a single cell of origin, can be readily isolated as a colony grown on semisolid agar-containing medium (Figure 1.14). Because bacterial colonies containing as many as 108 cells can develop overnight, selecting genetic variants of an E. coli strain-for example, mutants that are resistant to an antibiotic, such as penicillin-is easy and rapid. The ease with which such mutants can be selected and analyzed was critical to the success of experiments that defined the basic principles of molecular genetics, discussed in Chapter 3.
The nutrient mixtures in which E. coli divide most rapidly include glucose, salts, and various organic compounds, such as amino acids, vitamins, and nucleic acid precursors. However, E. coli can also grow in much simpler media consisting only of salts, a source of nitrogen (such as ammonia), and a source of carbon and energy (such as glucose). In such a medium, the bacteria grow a little more slowly (with a division time of about 40 minutes) because they must synthesize all their own amino acids, nucleotides, and other organic compounds. The ability of E. coli to carry out these biosynthetic reactions in simple defined media has made them extremely useful in elucidating the biochemical pathways involved. Thus, the rapid growth and simple nutritional requirements of E. coli have greatly facilitated fundamental experiments in both molecular biology and biochemistry.
Although bacteria have been an invaluable model for studies of many conserved properties of cells, they obviously cannot be used to study aspects of cell structure and function that are unique to eukaryotes. Yeasts, the simplest eukaryotes, have a number of experimental advantages similar to those of E. coli. Consequently, yeasts have provided a crucial model for studies of many fundamental aspects of eukaryotic cell biology.
The genome of the most frequently studied yeast, Saccharomyces cerevisiae, consists of 12 million base pairs of DNA and contains about 6000 genes. Although the yeast genome is approximately three times larger than that of E. coli, it is far more manageable than the genomes of more complex eukaryotes, such as humans. Yet even in its simplicity, the yeast cell exhibits the typical features of eukaryotic cells (Figure 1.15): It contains a distinct nucleus surrounded by a nuclear membrane, its genomic DNA is organized as 16 linear chromosomes, and its cytoplasm contains a cytoskeleton and subcellular organelles.
Yeasts can be readily grown in the laboratory and can be studied by many of the same molecular genetic approaches that have proved so successful with E. coli. Although yeasts do not replicate as rapidly as bacteria, they still divide as frequently as every 2 hours and can easily be grown as colonies from a single cell. Consequently, yeasts can be used for a variety of genetic manipulations similar to those that can be performed using bacteria.
These features have made yeast cells the most approachable eukaryotic cells from the standpoint of molecular biology. Yeast mutants have been important in understanding many fundamental processes in eukaryotes, including DNA replication, transcription, RNA processing, protein sorting, and the regulation of cell division, as will be discussed in subsequent chapters. The unity of molecular cell biology is made abundantly clear by the fact that the general principles of cell structure and function revealed by studies of yeasts apply to all eukaryotic cells.
Dictyostelium discoideum is a cellular slime mold, which, like yeast, is a comparatively simple unicellular eukaryote. The genome of Dictyostelium is approximately ten times larger than that of E. coli-more complex than the yeast genome but considerably simpler than the genomes of higher eukaryotes. Moreover, Dictyostelium can be readily grown in the laboratory and is amenable to a variety of genetic manipulations.
Under conditions of plentiful food, Dictyostelium lives as a single-celled amoeba, feeding on bacteria and yeasts. It is a highly mobile cell, and this property has made Dictyostelium an important model for studying the molecular mechanisms responsible for animal cell movements (Figure 1.16). For example, introducing the appropriate mutations into Dictyostelium has revealed the roles of several genes in cell motility.
An additional interesting feature of Dictyostelium is the ability of single cells to aggregate into multicellular structures. If an adequate supply of food is not available, the cells associate to form wormlike structures called slugs, each consisting of up to 100,000 cells that function as a unit. Dictyostelium thus appears to straddle the border between unicellular and multicellular organisms, providing an important model for studies of cell signaling and cell-cell interactions.
The unicellular eukaryotes Saccharomyces and Dictyostelium are important models for studies of eukaryotic cells, but understanding the development of multicellular organisms requires the experimental analysis of plants and animals, organisms that are more complex. The nematode Caenorhabditis elegans (Figure 1.17) possesses several notable features that make it one of the most widely used models for studies of animal development and cell differentiation.
Although the genome of C. elegans (approximately 100 million base pairs) is larger than those of unicellular eukaryotes, it is simpler and more manageable than the genomes of most animals. Its complete sequence has been determined, revealing that the genome of C. elegans contains approximately 19,000 genes-about three times the number of genes in yeast, and one-fifth the number of genes predicted in humans. Biologically, C. elegans is also a relatively simple multicellular organism: Adult worms consist of only 959 somatic cells, plus 1000 to 2000 germ cells. In addition, C. elegans can be easily grown and subjected to genetic manipulations in the laboratory.
The simplicity of C. elegans has enabled the course of its development to be studied in detail by microscopic observation. Such analyses have successfully traced the embryonic origin and lineage of all the cells in the adult worm. Genetic studies have also identified some of the mutations responsible for developmental abnormalities, leading to the isolation and characterization of critical genes that control nematode development and differentiation. Importantly, similar genes have also been found to function in complex animals (including humans), making C. elegans an important model for studies of animal development.
Like C. elegans, the fruit fly Drosophila melanogaster (Figure 1.18) has been a crucial model organism in developmental biology. The genome of Drosophila is similar in size to that of C. elegans, and Drosophila can be easily maintained and bred in the laboratory. Furthermore, the short reproductive cycle of Drosophila (about 2 weeks) makes it a very useful organism for genetic experiments. Many fundamental concepts of genetics-such as the relationship between genes and chromosomes-were derived from studies of Drosophila early in the twentieth century (see Chapter 3).
Extensive genetic analysis of Drosophila has uncovered many genes that control development and differentiation, and current methods of molecular biology have allowed the functions of these genes to be analyzed in detail. Consequently, studies of Drosophila have led to striking advances in understanding the molecular mechanisms that govern animal development, particularly with respect to formation of the body plan of complex multicellular organisms. As with C. elegans, similar genes and mechanisms exist in vertebrates, validating the use of Drosophila as a major experimental model in contemporary developmental biology.
The study of plant molecular biology and development is an active and expanding field of considerable economic importance as well as intellectual interest. Since the genomes of plants cover a range of complexity comparable to that of animal genomes (see Table 1.2), an optimal model for studies of plant development would be a relatively simple organism with some of the advantageous properties of C. elegans and Drosophila. The small flowering plant Arabidopsis thaliana (Figure 1.19) meets these criteria and is therefore widely used as a model to study the molecular biology of plants.
Arabidopsis is notable for its genome of only about 130 million base pairs-a complexity similar to that of C. elegans and Drosophila. In addition, Arabidopsis is relatively easy to grow in the laboratory, and methods for molecular genetic manipulations of this plant have been developed. These studies have led to the identification of genes involved in various aspects of plant development, such as the development of flowers. Analysis of these genes points to clear similarities between the mechanisms that control the development of plants and animals, further emphasizing the fundamental unity of cell and molecular biology.
The most complex animals are the vertebrates, including humans and other mammals. The human genome is approximately 3 billion base pairs-about 30 times larger than the genomes of C. elegans, Drosophila, or Arabidopsis. Moreover, the human body is composed of more than 200 different kinds of specialized cell types. This complexity makes the vertebrates difficult to study from the standpoint of cell and molecular biology, but much of the interest in biological sciences nonetheless stems from the desire to understand the human organism. Moreover, an understanding of many questions of immediate practical importance (e.g., in medicine) must be based directly on studies of human (or closely related) cell types.
One important approach to studying human and other mammalian cells is to grow isolated cells in culture, where they can be manipulated under controlled laboratory conditions. The use of cultured cells has allowed studies of many aspects of mammalian cell biology, including experiments that have elucidated the mechanisms of DNA replication, gene expression, protein synthesis and processing, and cell division. Moreover, the ability to culture cells in chemically defined media has allowed studies of the signaling mechanisms that normally control cell growth and differentiation within the intact organism.
The specialized properties of some highly differentiated cell types have made them important models for studies of particular aspects of cell biology. Muscle cells, for example, are highly specialized to undergo contraction, producing force and movement. Because of this specialization, muscle cells are a crucial model for studying cell movement at the molecular level. Another example is provided by nerve cells (neurons), which are specialized to conduct electrochemical signals over long distances. In humans, nerve cell axons may be more than a meter long, and some invertebrates, such as the squid, have giant neurons with axons as large as 1 mm in diameter. Because of their highly specialized structure and function, these giant neurons have provided important models for studies of ion transport across the plasma membrane, and of the role of the cytoskeleton in the transport of cytoplasmic organelles.
The frog Xenopus laevis is an important model for studies of early vertebrate development. Xenopus eggs are unusually large cells, with a diameter of approximately 1 mm (Figure 1.20). Because those eggs develop outside of the mother, all stages of development from egg to tadpole can be readily studied in the laboratory. In addition, Xenopus eggs can be obtained in large numbers, facilitating biochemical analysis. Because of these technical advantages, Xenopus has been widely used in studies of developmental biology and has provided important insights into the molecular mechanisms that control development, differentiation, and embryonic cell division.
The zebrafish (Figure 1.21) possesses a number of advantages for genetic studies of vertebrate development. These small fish are easy to maintain in the laboratory and they reproduce rapidly. In addition, the embryos develop outside of the mother and are transparent, so that early stages of development can be easily observed. Powerful methods have been developed to facilitate the isolation of mutations affecting zebrafish development, and several thousand such mutations have now been identified. Because the zebrafish is an easily studied vertebrate, it promises to bridge the gap between humans and the simpler invertebrate systems, such as C. elegans and Drosophila.
Among mammals, the mouse is the most suitable for genetic analysis. Although the technical difficulties in studying mouse genetics (compared, for example, to the genetics of yeasts or Drosophila) are formidable, several mutations affecting mouse development have been identified. Most important, recent advances in molecular biology have enabled the production of transgenic mice, in which specific mutant genes have been introduced into the mouse germ line, so that their effects on development or other aspects of cell function can be studied in the context of the whole animal. The suitability of the mouse as a model for human development is illustrated by the fact that mutations in homologous genes result in similar developmental defects in both species; piebaldism is a striking example (Figure 1.22).