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.