The Bacterial Genome

The genetic instructions for a cell are found in the DNA molecules. All DNA is derived from four different kinds of monomers, which we call nucleotides. DNA molecules are
double-stranded: two polymer chains are coiled together, their nucleotide units being associated as nucleotide pairs (see Fig. 5-7). The genetic messages in the DNA are in the form of sequences of nucleotides. These sequences usually consist of a series of code “words” or codons. Each codon is composed of three successive nucleotides and specifies which one of the 20 different kinds of amino acids will be used at a particular location in a protein. The sequence of codons in the DNA tells a cell how to order the amino acids for construction of its many
different proteins.

Transmission electron micrograph of a dividing cell of Escherichia coli O157:H7 attached to the intestinal epithelium of a neonatal calf. These bacteria, which are able to efface the intestinal microvilli, form characteristic attachments, and secrete shiga toxins, are responsible for ~73,000 illnesses and 60 deaths per year in the U. S. 10a After embedding, the glutaraldehyde-fixed tissue section was immunostained with goat anti-O157 IgG followed by protein A conjugated to 10-nm gold particles. These are seen around the periphery of the cell bound to the O-antigen (see Fig. 8-28). Notice the two microvilli of the epithelium. Courtesy of Evelyn A. Dean-Nystrom, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA.

A cell of a Spirillum negatively stained with
phosphotungstic acid. Note the tufts of flagella at the ends,
the rough appearance of the outer surface, the dark granules
of poly- -hydroxybutyric acid and the light-colored gran-
ules of unknown nature. Courtesy of F. D. Williams, Gail E.
VanderMolen, and C. F. Amstein.

Assume that a typical protein molecule consists of a folded chain of 400 amino acids. Its structural gene will therefore be a sequence of 1200 nucleotide pairs. Allowing a few more nucleotides to form spacer regions between genes we can take ~1300 as the number of
nucleotide pairs in a typical bacterial gene. However, some genes may be longer and some may be much shorter. The genome is the quantity of DNA that carries a complete set of genetic instructions for an organism. In bacteria, the genome is a single chromosome con-
sisting of one double-stranded DNA molecule. Mycoplasma genitalium is the smallest organism for which the DNA sequence is known. 11 Its genome is a double-
helical DNA circle of 580,070 nucleotide pairs and appears to contain about 480 genes (an average of ~1200 nucleotides per gene). The average mass of a nucleotide pair (as the
disodium salt) is 664 Da. It follows that the DNA of M. genitalium has a mass of ~385 x 106 Da. The relative molecular mass (Mr) is 0.385 x 109 (See Box 1-B for definitions of dalton and Mr). The DNA of E.coli is about seven times larger with a mass of ~2.7 x 109 Da. It contains ~4.2 x 106 nucleotide pairs and encodes over 4000 different proteins (see Table 1-3). Each nucleotide pair contributes 0.34 nm to the length of the DNA molecule; thus, the total length of DNA of an E. coli chromosome is 1.4 mm. This is about 700 times the length of the cell which contains it. Clearly, the molecules of DNA are highly folded, a fact that accounts for their appearance in the electron microscope as dense aggregates called nucleoids, which occupy about one-fifth of the cell volume. Each bacterial nucleoid contains a complete set of genetic“blueprints” and functions independently. Each nucleoid is haploid, meaning that it contains only a single complete set of genes. In addition to their chromosome, bacteria often contain smaller DNA molecules known as plasmids. These plasmids also carry genetic information that may be useful to bacteria. For example, they often encode proteins that confer resistance to antibiotics. The ability to acquire new genes from plasmids is one mechanism that allows bacteria to adapt readily to new environments.
Plasmids are also used in the laboratory in the cloning of genes and in genetic engineering.

(A) Thin (~60 nm) section of an aquatic gram-
negative bacterium, Aquaspirillum fasciculus. Note the light-
colored DNA, the dark ribosomes, the double membrane
characteristics of gram-negative bacteria (Chapter 8, Section
E), and the cell wall. In addition, an internal “polar mem-
brane” is seen at the end. It may be involved in some way in
the action of the flagella. (B) A thin section of dividing cell
of Streptococcus, a gram-positive organism. Note the DNA
(light-stranded material). A portion of a mesosome is seen
in the center and septum can be seen forming between the
cells. Micrographs courtesy of F. D. Williams, Gail E.
VanderMolen, and C. F. Amstein.