Chapter 2:  The Nature of Genomes

Genome Size

One basic questions that needs to be answered is “How big are genomes?” Genome sizes are measured in units of thousands of nucleotide pairs (called kilobases, kb) or millions of nucleotide pairs (megabases, mb). Figure 2-7 shows the size ranges of representative genomes. Notice that generally genome size increases with complexity of the group, but there is considerable variation (up to a thousandfold!) in some of the groups. Table 2-2 compares sizes of representative genomes and genomic components. The table also shows the number of genes in these examples. The number of genes is roughly proportional to genome size, but there are discrepancies caused by repetitive DNA and introns. Viruses and plasmids, neither of which are capable of independent existence, contain the smallest number of genes.

We now turn to a detailed discussion of various genomes in order of increasing size.

Plasmid Genomes

Bacterial cells isolated from nature often contain small DNA elements that are not essential for the basic operation of the bacterial cell. These elements are called plasmids. Plasmids are symbiotic molecules that cannot survive at all outside of cells. Even though plasmids are not part of the basic operational system of their host cells, some are quite complex, carrying many genes, so it is quite appropriate to refer to their distinctive DNA as a “plasmid genome.” Bacterial plasmids often contain genes that are extremely useful to the bacterial host, for example, by promoting bacterial cell fusion, conferring antibiotic resistance, or producing toxins.

Plasmids also are occasionally found in fungal and plant cells. Most are found inside mitochondria and chloroplasts, but some are found in nuclei or in the cytosol. Unlike the bacterial plasmids mentioned above, these eukaryotic plasmids seem to provide no benefits for their hosts—they seem to exist selfishly, only for the purpose of their own propagation.

For their replication and maintenance, plasmids depend on the general cellular machinery encoded by the host genome. Bacterial plasmids are most often circular, but there are linear types too. In fungi and plants, linear plasmids are most common, but circular types are known in fungi.

Organellar DNA

The bulk of the eukaryotic genome is contained within the chromosomes in the nucleus. However in addition to the nuclear DNA, some cellular organelles—mitochondria and chloroplasts—also contain an organelle-specific chromosomal type. Mitochondrial and chloroplast chromosomes consist of double-stranded DNA molecules. Individual mitochondria and chloroplasts contain identical multiple copies of their chromosomes, and each cell contains several to many of these organelles. Therefore the copy number of these chromosomes per cell can be quite high, often in the hundreds. Hence the DNA is relatively easy to extract from organelle fractions of disrupted cells. The organelle chromosomes contain genes specific to the functions of the organelle concerned. Nevertheless, most of the biological functions that occur inside these organelles are specified by genes in the nuclear genome. There is no overlap with the nuclear genome in gene content. Mitochondria and chloroplasts probably were originally prokaryotic cells that entered and took up a symbiotic relationship inside another cell (according to the endosymbiotic theory of eukaryotic origin). Throughout evolution most of the original prokaryotic genes were transferred to the nuclear genome or lost. Mitochondrial genomes can be eliminated in some organisms such as yeasts (which can switch to fermentation reactions to obtain energy), but most organisms cannot survive without them, so there is still mutual interdependence between nuclear and organelle subdivisions of the genome. Chloroplasts can be eliminated only in photosynthetic organisms that can survive by taking in preformed nutrients from the environment (that is, that can act as heterotrophs). Analysis of organellar genomes shows that they are inherently circular, but linearized forms of these genomes can be detected in cells. Many organelle genes have introns.

Viral Genomes

A virus is a nonliving particle that can reproduce itself only by infecting a living cell and subverting the cellular machinery of its host cell to generate progeny viral particles. Viruses of bacteria are also called bacteriophages (literally, “eaters of bacteria”). Viruses are composed of a protein coat and a core that contains its genome. During infection, the viral genome enters the cell, mediated by either a merger of the viral coat with the plasma membrane of the cell or by a syringe-like injection process.

There is thus an intracellular phase to the replication cycle of the viral genome, as well as a phase in which it is packaged into the infective viral particle. Since it is easier to purify the viral genome when it is contained in the extracellular viral particle, viral genomes are usually described in terms of their structure as found in the viral particle. Viral genomes are quite varied. The genomes of many viruses are composed of DNA. When packaged into the viral particle, in some viruses the DNA is double-stranded, in other cases single-stranded. Still other viruses, such as the retroviruses (HIV is an example), have RNA genomes in the viral particle. Again, sometimes these RNA genomes are single-stranded, in other cases double-stranded. Some viral genomes contain linear DNA or RNA molecules, whereas others are circular.

Thus, we see a much greater diversity in the kinds of molecules that form the viral genomes compared with the double-stranded DNA genomes found in all living cells. This diversity is based partly on the various special strategies for packing the genome into infective viral particles and partly on the diverse evolutionary histories of viruses. Regardless of the nature of the viral genome that is packaged in the infective particle, there is a phase of the life history of the viral genome inside the cell when it is converted into a double-stranded DNA molecule, in other words, into the same sort of molecular structure as the host genome. Depending on the virus and the conditions in the cell, this intracellular form of the genome may be incorporated into a host chromosome or it may be a completely separate molecule. Most viral genes do not have introns.

In the small genomes of plasmids, organelles, and viruses, the genes are found close together with relatively little intergenic space. This is also true of prokaryotic genomes but contrasts with the chromosomes of many animals and plants, in which (as we shall see) there are often large stretches of DNA between the genes.

Unlike the organismal genomes, the small genomes do not have large amounts of protein associated with them. Linear viruses and linear plasmids have a special protein permanently attached to the 5′ phosphate group at each end; these proteins play a crucial role when the DNA replicates.

Electron micrographs of representative small genomes are shown in Figure 2-8.

Prokaryotic Genomes

The genome of most prokaryotes is contained within a single chromosome. For most prokaryotes, this chromosome is a single, closed, circular double helix of DNA. There are some exceptions, such as the bacterium Borrelia burgdorfei, in which the chromosome is a single linear DNA double helix. Some bacterial genomes consist of several different chromosomes.

Bacterial genes are arranged close together with little intergenic space, and introns are extremely rare. In some regions of prokaryotic genomes, some functionally related genes are located together as a group, and one molecule of mRNA is made from the entire unit; such a unit is termed an operon. The genes concerned with lactose utilization in the colon bacterium Escherichia coli constitute an operon and are transcribed as one mRNA molecule. Operons are very rare in eukaryotes. The functional properties of operons will be discussed in Chapter 14. Within each bacterial cell there can be from one to several identical copies of the single chromosome type.

In electron micrographs of bacterial cells the DNA is seen arranged in a dense clump called a nucleoid. When cells are broken, the packing of the nucleoid is lost and DNA tumbles out in a disorganized skein (Figure 2-9). Bacterial genomes have associated proteins that are thought to help package the genome into a nucleoid, but the precise functions of these DNA-associated proteins are not understood.

Eukaryotic Nuclear Genomes

In eukaryotic organisms, the vast majority of genes are found in the chromosomes of the nucleus (Figure 2-10). Most eukaryotic species are classified as either diploid, carrying two sets of nuclear chromosomes (two copies of the nuclear portion of the genome) in each nucleus in body cells, or haploid, with only one chromosome set per nucleus. Most fungi and algae are haploids, whereas most other eukaryotes, including animals and flowering plants, are diploids. However, it is worth noting that diploid organisms produce specialized haploid reproductive cells (such as ova and sperm in animals), and conversely haploid organisms produce specialized diploid cells during the sexual phase of their life cycles.

The letter n is used to designate the number of chromosomes in one nuclear genome, so the haploid condition is designated n (that is, 1 × n) and the diploid state is 2n (that is, 2 × n). The symbol n is called the haploid chromosome number. Conditions that are 3n, 4n, 5n, 6n, and so on are also known, especially in plants; these are called polyploids and will be discussed in Chapter 8. The number of chromosome sets (1, 2, 3, 4, 5, 6, etc.) is sometimes called the ploidy or ploidy level. Note that the ploidy level conventionally refers to the number of sets in a cell that has not entered cell division.

In a diploid cell, since there are two chromosome sets, there are two chromosomes of each type—two of chromosome 1, two of chromosome 2, two of chromosome 3, and so on. The members of a pair are called homologous chromosomes or homologs. Members of a homologous pair are substantially alike in size and gene content, carrying the same genes in the same relative positions. Hence a segment of a pair of homologous chromosomes in a diploid cell can be represented

However, a pair of homologs can carry different alleles of a gene (see the definition of allele in Chapter 1), and these would represent minor differences between the homologs. Chromosome numbers are determined simply by counting stained preparations under a light microscope. Chromosomes are easier to see when they are in a condensed form, as during cell division. Chromosome numbers of a sample of diploid organisms are given in Table 2-3.

Different chromosomes in the genome contain different sets of genes. This can be demonstrated by examining abnormal individuals that contain one extra chromosome. The extra chromosome produces an abnormal appearance that is characteristic for that chromosome, suggesting that each chromosome is different. An example from plants is shown in Figure 2-11. Mapping (Chapter 5) and sequencing (Chapter 12) of chromosomes has confirmed the idea that different chromosomes have distinctly different sets of genes. As we will see in the next section, chromosomes vary greatly in appearance under the microscope, and these unique diagnostic features also suggest strongly that the gene content of the different chromosomes varies.

Figure 2-12 on the next page is a diagrammatic summary of the main features of size and genetic organization of the various types of genomes discussed above.