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Journal of Bacteriology, September 2004, p. 5842-5855, Vol. 186, No. 17
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.17.5842-5855.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

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

Michael P. McLeod,1,2,{dagger} Xiang Qin,1,{dagger} Sandor E. Karpathy,1,2 Jason Gioia,3 Sarah K. Highlander,3 George E. Fox,4 Thomas Z. McNeill,1,4 Huaiyang Jiang,1 Donna Muzny,1 Leni S. Jacob,1 Alicia C. Hawes,1 Erica Sodergren,1 Rachel Gill,1 Jennifer Hume,1 Maggie Morgan,1 Guangwei Fan,1 Anita G. Amin,1 Richard A. Gibbs,1 Chao Hong,5 Xue-jie Yu,5 David H. Walker,5 and George M. Weinstock1,2,3*

Human Genome Sequencing Center,1 Department of Molecular Virology and Microbiology, Baylor College of Medicine,3 Department of Biology and Biochemistry, University of Houston,4 Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston,2 Department of Pathology, University of Texas Medical Branch, Galveston, Texas5

Received 17 February 2004/ Accepted 17 May 2004

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 Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii, indicating that this region is a hot spot for rearrangements.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.

* Corresponding author. Mailing address: Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030-7783. Phone: (713) 798-4357. Fax: (713) 798-4373. E-mail: gwstock{at}bcm.tmc.edu.

{dagger} M.P.M. and X.Q. contributed equally to this study.

Journal of Bacteriology, September 2004, p. 5842-5855, Vol. 186, No. 17
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.17.5842-5855.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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