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The α-proteobacteria Rickettsia prowazekii and Bartonella henselae are the causative agents of epidemic typhus and cat scratch disease respectively. Whereas R. prowazekii is an obligate intracellular parasite, B. henselae can live and proliferate both outside and inside the eukaryotic host cell. Besides the obvious medical interest to identify the complete gene set of two human pathogens, their genome sequences are also important for the study of evolutionary processes. Both R. prowazekii and B. henselae have small genomes, but their last common ancestor of these two bacteria was most likely a free-living organism with a substantially larger genome.

The aim of this thesis is to compare the complete genomes of R. prowazekii and B. henselae and to decipher the evolutionary processes leading to the adaptation to an intracellular lifestyle. The working hypothesis was that the facultative intracellular B. henselae is an intermediate between a free living bacteria and the obligate R. prowazekii, which is corroborated. B. henselae has a broader biosynthetic repertoire than R. prowazekii, including the presence of genes for glycolysis and de novo biosynthesis of purines and pyrimidines. However, both bacteria have reduced gene sets for biosynthesis of amino acids and cofactors compared to free-living bacteria.

Comparisons of gene order in bacteria reveal that several operons are well conserved between distantly related species. The genome sequences of R. prowazekii and B. henselae show that many of the operons that are usually conserved, are broken and rearranged in these species. One of the mechanisms of reductive evolution include intra-chromosomal recombination between repeated loci. This process expels one of the repeats and cause rearrangements in the gene order of the flanking regions. While the R. prowazekii genome almost completely lack repeated sequences, the B. henselae genome is rich in repeats. These repeats are, however, most often located within regions associated with pathogenicity islands. The higher number of scrambled operons, and the lower number of repeats, in R. prowazekii compared to B. henselae imply that the reductive process has gone further in the former species.

It has been suggested that Rickettsia Palindromic Elements (RPEs) have evolved as selfish DNA that mediate protein sequence evolution by being targeted to genes that code for RNA and proteins. Here, we have examined the phylogenetic depth of two RPEs that are located close to the genes encoding elongation factors Tu (tuf) and G (fus) in Rickettsia. An exceptional organization of the elongation factor genes was found in all 11 species examined, with complete or partial RPEs identified downstream of the tuf gene (RPE-tuf) in six species and of the fus gene (RPE-fus) in 10 species. A phylogenetic reconstruction shows that both RPE-tuf and RPE-fus have evolved in a manner that is consistent with the expected species divergence. The analysis provides evidence for independent loss of RPE-tuf in several species, possibly mediated by short repetitive sequences flanking the site of excision. The remaining RPE-tuf sequences evolve as neutral sequences in different stages of deterioration. Likewise, highly fragmented remnants of the RPE-fus sequence were identified in two species. This suggests that genome-specific differences in the content of RPEs are the result of recent loss rather than recent proliferation.

Species of the genus Rickettsia are obligate intracellular parasites of the a-proteobacterial subdivision. It has been suggested that obligate intracellular bacteria have evolved from free-living bacteria with much larger genome sizes. Transitions to intracellular growth habitats are normally associated with radical genomic alterations, particularly genome rearrangements and gene losses.

This thesis presents a comparative study of evolutionary processes such as gene rearrangements, deletions and duplications in a variety of Rickettsia species. The results show that early intrachromosomal recombination events mediated by duplicated genes and short repeats have resulted in deletions as well as rearrangements. For example, an exceptional organization of the elongation factor genes was found in all species examined, suggesting that this rearrangement event occurred at the early stage of the evolution of Rickettsia. Likewise, it was found that a repetitive element, the so-called Rickettsia Palindromic Element (RPE) flourished prior to species divergence in Rickettsia. Finally, a phylogenetic analysis shows that the duplication events that gave rise to the five genes encoding ATP/ADP transporters occurred long before the divergence of the two major groups of Rickettsia. Taken together, this suggests that Rickettsia have been intracellular parasites for an extensive period of time.

A detailed analysis of the patterns of nucleotide changes in genes and intergenic regions among the different species provides evidence for a gradual accumulation of short deletions. This suggests that different distributions of genes and repeated sequences in modern Rickettsia species reflect species-specific differences in rates of deterioration rather than variation in rates of intra-genomic sequence proliferation.