Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae.
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 Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii, indicating that this region is a hot spot for rearrangements.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.
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030-7783, USA.
Michael P
MP
McLeod
Xiang
X
Qin
Sandor E
SE
Karpathy
Jason
J
Gioia
Sarah K
SK
Highlander
George E
GE
Fox
Thomas Z
TZ
McNeill
Huaiyang
H
Jiang
Donna
D
Muzny
Leni S
LS
Jacob
Alicia C
AC
Hawes
Erica
E
Sodergren
Rachel
R
Gill
Jennifer
J
Hume
Maggie
M
Morgan
Guangwei
G
Fan
Anita G
AG
Amin
Richard A
RA
Gibbs
Chao
C
Hong
Xue-Jie
XJ
Yu
David H
DH
Walker
George M
GM
Weinstock
D007446:Chromosome Inversion; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D003576:Electron Transport Complex IV / Q000235:genetics; D018965:Frameshifting, Ribosomal; D015964:Gene Expression Regulation, Bacterial; D015321:Gene Rearrangement; D005798:Genes, Bacterial; D020459:Genes, rRNA; D016680:Genome, Bacterial; D023281:Genomics; D008969:Molecular Sequence Data; D011544:Pseudogenes; D012343:RNA, Transfer / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D012281:Rickettsia / Q000235:genetics; D020114:Rickettsia conorii / Q000235:genetics; D012286:Rickettsia typhi / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D026801:Synteny
D004269:DNA, Bacterial; D022661:RNA, Untranslated; D012343:RNA, Transfer; D003576:Electron Transport Complex IV