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Chapter 6 : Generating Intracellular Processes
For a bacterium short-term survival depends on the high fidelity of the replication machinery to prevent genomic alteration, but in the long term, evolution needs to occur. There are two basic themes, one providing for genome modification and the other providing for an increase in genomic content. The processes considered in this chapter are those of replication, amplification, and deletion. In fact, if gene acquisition, through transfer processes, is as high as is considered likely, then processes driving deletion reactions will be strategically important to conserving genome size. DNA sequences are subject to change for better or for worse, so selection would appear to favor individuals with a mutation rate approaching zero and an accurate replication machinery. Mutation is an event that is more likely to adversely effect the activity of a gene product. As mutations occur there is no mechanism for identifying them or replacing them by recombination. Clonal species are strongly driven by competition because one clone is "much like" another. This allows them to acquire by recombination large amounts of genetic sequence. Homology-independent (site-specific) pathways of DNA incorporation are likely to lead to increases in genome complexity. But nonhomologous (site-specific) recombination is also important in shaping bacterial genomes. Evidence suggests that gene elongation and duplication was the route taken by ancestral life forms to enlarge their genomes and increase their biochemical capacity. Genomic analysis of the three cell domains, Archaea, Bacteria, and Eukarya is allowing an analysis of their relationships.