In the early days of molecular biology, the spotlight focused intensely on just one species: the Escherichia coli, or E. coli, bacterium (see Figures 1–13 and 1–14). This small, rod-shaped bacterial cell normally lives in the gut of humans and other vertebrates, but it can be grown easily in a simple nutrient broth in a culture bottle. It adapts to variable chemical conditions and reproduces rapidly, and it can evolve by mutation and selection at a remarkable speed. As with other bacteria, different strains of E. coli, though classified as members of a single species, differ genetically to a much greater degree than do different varieties of a sexually reproducing organism such as a plant or animal. One E. coli strain may possess many hundreds of genes that are absent from another, and the two strains could have as little as 50% of their genes in common. The standard laboratory strain
E. coli K-12 has a genome of approximately 4.6 million nucleotide pairs, contained in a single circular molecule of DNA that codes for about 4300 different kinds of proteins (Figure 1–24).
In molecular terms, we know more about E. coli than about any other living organism. Most of our understanding of the fundamental mechanisms of life— for example, how cells replicate their DNA, or how they decode the instructions represented in the DNA to direct the synthesis of specific proteins—initially came from studies of E. coli. The basic genetic mechanisms have turned out to be highly conserved throughout evolution: these mechanisms are essentially the same in our own cells as in E. coli.
Prokaryotes (cells without a distinct nucleus) are biochemically the most diverse organisms and include species that can obtain all their energy and nutrients from inorganic chemical sources, such as the reactive mixtures of minerals released at hydrothermal vents on the ocean floor—the sort of diet that may have nourished the first living cells 3.5 billion years ago. DNA sequence comparisons reveal the family relationships of living organisms and show that the prokaryotes fall into two groups that diverged early in the course of evolution: the bacteria (or eubacteria) and the archaea. Together with the eukaryotes (cells with a membrane-enclosed nucleus), these constitute the three primary branches of the tree of life.
Most bacteria and archaea are small unicellular organisms with compact genomes comprising 1000–6000 genes. Many of the genes within a single organism show strong family resemblances in their DNA sequences, implying that they originated from the same ancestral gene through gene duplication and divergence. Family resemblances (homologies) are also clear when gene sequences are compared between different species, and more than 200 gene families have been so highly (A) 4,639,221 nucleotide pairs Escherichia coli K-12 origin of replication terminus of replication (B)
Figure 1–24 The genome of E. coli. (A) A cluster of E. coli cells. (B) A diagram of the genome of
E. coli strain k-12. The diagram is circular because the dnA of E. coli, like that of other prokaryotes, forms a single, closed loop. Protein-coding genes are shown as yellow or orange bars, depending on the dnA strand from which they are transcribed; genes encoding only RnA molecules are indicated by green arrows. some genes are transcribed from one strand of the dnA double helix (in a clockwise direction in this diagram), others from the other strand (counterclockwise). (A, courtesy of dr. Tony Brain and david Parker/Photo Researchers; B, adapted from F.R. Blattner et al., Science 277:1453–1462, 1997.) conserved that they can be recognized as common to most species from all three domains of the living world. Thus, given the DNA sequence of a newly discovered gene, it is often possible to deduce the gene’s function from the known function of a homologous gene in an intensively studied model organism, such as the bacterium
E. coli.