Genome degradation is an ongoing process in Rickettsia

To study reductive evolutionary processes in bacterial genomes, we examine sequences in the Rickettsia genomes which are unconstrained by selection an d evolve as pseudogenes, one of which is the metK gene, which codes for Ado Met synthetase. Here, we sequenced the metK gene and three surrounding gene s in eight different species of the genus Rickettsia. The metK gene was fou nd to contain a high incidence of deletions in six lineages, while the thre e genes in its surroundings were functionally conserved in all eight lineag es. A more drastic example of gene degradation was identified in the metK d ownstream region, which contained an open reading frame in Rickettsia felis . Remnants of this open reading frame could be reconstructed in five additi onal species by eliminating sites of frameshift mutations and termination c odons. A detailed examination of the two reconstructed genes revealed that deletions strongly predominate over insertions and that there is a strong t ransition bias for point mutations which is coupled to an excess of GC-to-A T substitutions. Since the molecular evolution of these inactive genes shou ld reflect the rates and patterns of neutral mutations, our results strongl y suggest that there is a high spontaneous rate of deletions as well as a s trong mutation bias toward AT pairs in the Rickettsia genomes. This may exp lain the low genomic G+C content (29%), the small genome size (1.1 Mb), and the high noncoding content (24%), as well as the presence of several pseud ogenes in the Rickettsia prowazekii genome.