Comparative Genomics of Endosymbiotic Bacteria

Abstract: Genomes of intracellular bacteria are thought to be the products of reductive evolution. They have evolved from ancestral genomes of free-living bacteria through a process of massive gene loss. This doctoral thesis focuses on the comparison of the only two completely sequenced genomes of obligate symbionts presently available: Buchnera (Ap) and Buchnera (Sg). The sequencing of the complete genome of Buchnera (Sg) is a part of this work.A major finding presented is that these genomes are remarkably conserved in both genome content and gene order, which contrasts with the current view of bacterial genomes as rapidly evolving entities. On the basis of the data obtained, there are no signs of inversions, translocations, duplications or horizontally transferred genes. Furthermore, the Buchnera genomes are the first bacterial genomes identified with a loss of recA, a major gene involved in homologous recombination. This single deletion event has probably contributed to the observed genomic stasis. In addition, the recF gene involved in DNA-repair and SOS induction has also been eliminated, and mutations have started to accumulate in genes related to base-excision repair in Buchnera (Sg). In contrast to the remarkable stability in structure, surprisingly high rates of nucleotide substitutions causing amino acids replacements and substitutions at synonymous sites were identified. Therefore, the genetic changes introduced into these two genomes since their divergence is almost exclusively due to the nucleotide sequence substitutions.A number of pseudogenes in different stages of gene degradation have been observed in the Buchnera (Sg) genome, suggesting that genome reduction is still an ongoing, albeit slow process. Almost half of the weakly mutated genes with single or a few frameshift mutations are associated with DNA-repair, cell envelope or cysteine biosynthesis. A comparative study of a set of genes involved in peptidoglycan biosynthesis in four additional lineages of Buchnera has shown that some of the single nucleotide deletions were acquired already 30-50 million years ago. Nevertheless, the substitution patterns of these genes are typical of Buchnera genes, suggesting that they may have maintained a functional role despite the accumulation of frameshift mutations.The two Buchnera genomes are the first ever completely sequenced bacterial genomes for which a divergence date is available (50-70 myr). This was made possible by the availability of a fossil record for the aphid host and the exclusively vertical transmission of Buchnera via maternal inheritance. Thus, the analysis of the two genomes provides a first insight into the pace of molecular evolution in prokaryotes. Substitution rates were estimated to 9 x 10-9 synonymous substitutions per site and per year and 1.65 x 10-9 nonsynonymous substitutions per site and per year on the average for all orthologous genes identified in the genomes. The rate of gene loss was found to be surprisingly low, with about one complete gene elimination per 5-10 million years.