FEATURE ARTICLE
The Evolutionary Ecology of Escherichia coli
Abundantly studied and much feared, E. coli has more genomic plasticity than once believed and may have followed various routes to become a pathogen
Valeria Souza, Amanda Castillo, Luis Eguiarte
Clues in the Genome
Our familiarity with E. coli comes from our intimate experience with it as well as its widespread use as a workhorse in the genetics laboratory. E. coli lives in the gut of human beings and of many other mammals, domestic and wild; it also lives elsewhere in nature. E. coli makes headlines when a pathogenic strain contaminates food or drink, but in fact there are many benign strains living unnoticed among our normal intestinal fauna and in our environment.
E. coli is a member of the Enterobacteriaceae family. Molecular phylogeny studies indicate that it is closely related to some other pathogens of vertebrates, including Shigella and Salmonella, the Vibrio cholera bacteria and Haemophilus, which can cause pneumonia and meningitis. The enterobacteria are characterized by their capacity for facultative respiration: They are aerobic in the open air but live anaerobically inside the gut. Thanks to this versatility, many members of this family are free-living, whereas others live in commensal relationships with animals or plants.
A harmless strain of E. coli called K-12, widely used in genetic-engineering experiments, has been well studied, and the genome of one variant has been sequenced by Frederick R. Blattner and his colleagues at the E. coli Genome Project at the University of Wisconsin-Madison. This strain contains 4,639,221 base pairs, or 4.6 megabases, of double-stranded circular DNA (compared with the 3 billion base pairs of chromosomal DNA in the human genome). Of this genome 87.8 percent codes for proteins, and 0.8 percent codes for RNAs, or ribonucleic acids, key workers in protein synthesis. Another 0.7 percent consists of DNA without any known function. It is estimated that around 11 percent of the chromosome has regulatory functions. Some 28 percent of the 4,288 open reading frames (arrays coding for proteins) have no known function.
Other strains of E. coli may have differences in their genomic structure; it is now suspected that the maps are not always colinear and that the size of the genome varies from 4.4 to 5.5 megabases. The other strain that has been sequenced, a dangerous enterohemorrhagic E. coli (EHEC) known as O157:H7, appears to have acquired many of its genes by horizontal transfer since it diverged from K-12 about 4 million years ago. Horizontal or lateral gene transfer is a special talent of bacteria, which can exchange DNA within or across species lines. Such gene-swapping takes place through bacterial conjugation, when two bacteria join and share DNA; through the intervention of bacteriophages, or bacteria-infecting viruses; or through transformation, wherein they take up "loose" DNA from their environment.
O157:H7, the culprit in several recent fatal outbreaks of foodborne disease in the U.S. and Europe, turns out to have 1,387 genes that K-12 lacks; these include virulence factors, certain metabolic pathways and prophages (DNA acquired from viruses), as well as genes enabling DNA elements to move around on a chromosome. It is remarkable that a strain can have so many novel genes; these comprise some 25 percent of the O157:H7 genome. By comparison, all human beings are thought to be genetically about 99 percent identical.
When they released the O157:H7 sequence last year, Nicole T. Perna of Blattner's group at the University of Wisconsin and her colleagues noted that a comparison of the K-12 and O157:H7 genomes shows that the enterobacteria are the subjects of a great deal more genetic recombination, or scrambling of genes, than had been suspected. Lateral transfer creates bacterial genomes that are mosaics of genes with different evolutionary histories. For example, geneticists can find markers of inheritance by looking for patterns in the nucleotide bases that link to form double-stranded DNA. One common statistic is the proportion of base pairs that have the arrangement G-C, in which the bases guanine and cytosine are linked. The E. coli genome on average consists of 50.8 percent G-C pairs. But a number of important genes (15 percent of the K-12 genome and 26 percent of the O157:H7 genome) contain different G-C proportions from the rest of the genome and also use codons (triplets of bases coding for a single amino acid) in a very different way. For this reason it has been suggested that these genes came from other bacterial lines and were acquired by E. coli recently via horizontal transfer.
Jeffrey G. Lawrence of the University of Pittsburgh and Howard Ochman of the University of Arizona in Tucson in 1998 estimated the rate of these transfers to be at least in the range of 16 kilobases every million years; "pathogenic islands" (regions where genes that confer pathogenicity are found) dominate this activity.
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