The Dynamic Bacterial Genome

Abstract

The model of a static bacterial chromosome arose from early comparisons of the genetic maps of Escherichia coli and Salmonella typhimurium. Analyses of complete genome sequences by several methods revealed that the differences in gene content were the result of two complementary processes: the gain of new genes by horizontal gene transfer from distantly related organisms, and the loss of ancestral genes from descendent lineages. Directional mutation pressures provide a distinct ‘‘fingerprint’’ to a bacterial genome owing to the differential mutational proclivities of DNA polymerases, the nature and number of mismatch correction systems, the numbers and abundances of tRNA species, and even relative concentrations of precursor nucleotide pools. Thus, genes which appear atypical in their current genomic context may reflect the direction pressures of a donor genome. Aside from changes in gene content, gene order has also been found to be more plastic than once assumed. Mechanisms for DNA rearrangement are well known and have been well measured in the laboratory. Yet despite the opportunities for chromosomal rearrangement, the genetic maps of E. coli and S. enterica seemed to be largely congruent, save the inversion about the terminus of replication. The genome, with all its dynamic parts, steers the organism into the environmental space it is best suited to exploit. Rather than a stale collection of genes having reached optimal performance after billions of years of evolution, one may view a bacterial genome as an ever-changing consortium of genes which cooperate in perpetuating their host organism.