chapter  15
Genomes III: Bacteria and Archaea
Pages 12

Escherichia coli has been one of the most intensively studied of all bacteria. Most of the genetic mechanisms that are known rst were examined in this microbe. The genome of E. coli K12 is 4,639,221 bp in length, which contains 4,289 protein-coding genes (Table 15.1 and Figure 15.1), 114 tRNA genes, and 7 rRNA operons (each containing a 16S, 23S, and 5S gene), plus an additional 5S gene. This bacterium grows in the intestines of animals, where conditions are anaerobic. However, it can survive for long periods outside of the animals and, thus, can live in aerobic conditions as well. The greatest proportion of the genome (by function) is devoted to energy metabolism. There are genes that allow E. coli to grow under both aerobic and anaerobic conditions. It has genes that encode proteins for energy metabolism, including those involved in glycolysis, ATP synthase, electron transport, the TCA cycle, sugar utilization, methanogenesis, fermentation, and others. It even has four genes that normally are used in photosynthesis, although they must be used in a different way by this nonphotosynthetic organism. The portion of the genome that has the second highest number of genes is transporters and binding proteins. In order to survive both inside and outside of the animals, E. coli has additional transporters, which allows a greater variety of molecules to be imported and exported, and allows greater £exibility in where E. coli can grow. For example, it has more anionic and cationic transporters, which allows it to grow under a wider range of pH conditions than cells species with fewer transporters. The third most numerous category

of genes is transcription, including proteins that control transcription. While the number of genes for RNA polymerase, helicase, and accessory proteins is about the same, the number of transcription regulators and factors is higher than in bacteria with smaller genomes. This is because the variety of genes that allows E. coli to grow under many different conditions. However, it must be able to sense and respond to each of those conditions appropriately by turning on specic sets of genes while suppressing expression of other genes. The transcriptional regulators and factors perform these functions. The fourth largest portion of the genome involves DNA replication and cell division. Compared to smaller genomes, there are more genes for nucleic acid synthesis, DNA replication, recombination, and repair. All of these increase the delity of DNA replication, and help to maintain the larger genome of this organism.