Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae

Abstract

ABSTRACT Rickettsia typhi , the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome sequence of R. typhi (1,111,496 bp) and compare it to the two published rickettsial genome sequences: R. prowazekii and R. conorii . We identified 877 genes in R. typhi encoding 3 rRNAs, 33 tRNAs, 3 noncoding RNAs, and 838 proteins, 3 of which are frameshifts. In addition, we discovered more than 40 pseudogenes, including the entire cytochrome c oxidase system. The three rickettsial genomes share 775 genes: 23 are found only in R. prowazekii and R. typhi , 15 are found only in R. conorii and R. typhi , and 24 are unique to R. typhi . Although most of the genes are colinear, there is a 35-kb inversion in gene order, which is close to the replication terminus, in R. typhi , compared to R. prowazekii and R. conorii . In addition, we found a 124-kb R. typhi -specific inversion, starting 19 kb from the origin of replication, compared to R. prowazekii and R. conorii . Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii , indicating that this region is a hot spot for rearrangements. Genome comparisons also revealed a 12-kb insertion in the R. prowazekii genome, relative to R. typhi and R. conorii , which appears to have occurred after the typhus ( R. prowazekii and R. typhi ) and spotted fever ( R. conorii ) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae.