title: The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes.
abstract: Scrub typhus is caused by the obligate intracellular rickettsia Orientia tsutsugamushi (previously called Rickettsia tsutsugamushi). The bacterium is maternally inherited in trombicuid mites and transmitted to humans by feeding larvae. We report here the 2,127,051-bp genome of the Boryong strain, which represents the most highly repeated bacterial genome sequenced to date. The repeat density of the scrub typhus pathogen is 200-fold higher than that of its close relative Rickettsia prowazekii, the agent of epidemic typhus. A total of 359 tra genes for components of conjugative type IV secretion systems were identified at 79 sites in the genome. Associated with these are >200 genes for signaling and host-cell interaction proteins, such as histidine kinases, ankyrin-repeat proteins, and tetratrico peptide-repeat proteins. Additionally, the O. tsutsugamushi genome contains >400 transposases, 60 phage integrases, and 70 reverse transcriptases. Deletions and rearrangements have yielded unique gene combinations as well as frequent pseudogenization in the tra clusters. A comparative analysis of the tra clusters within the genome and across strains indicates sequence homogenization by gene conversion, whereas complexity, diversity, and pseudogenization are acquired by duplications, deletions, and transposon integrations into the amplified segments. The results suggest intragenomic duplications or multiple integrations of a massively proliferating conjugative transfer system. Diversifying selection on host-cell interaction genes along with repeated population bottlenecks may drive rare genome variants to fixation, thereby short-circuiting selection for low complexity in bacterial genomes.
authors.affiliation: Department of Microbiology and Immunology, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul 110-799, Republic of Korea.
authors.forename: Nam-Hyuk
authors.initials: NH
authors.lastname: Cho
authors.forename: Hang-Rae
authors.initials: HR
authors.lastname: Kim
authors.forename: Jung-Hee
authors.initials: JH
authors.lastname: Lee
authors.forename: Se-Yoon
authors.initials: SY
authors.lastname: Kim
authors.forename: Jaejong
authors.initials: J
authors.lastname: Kim
authors.forename: Sunho
authors.initials: S
authors.lastname: Cha
authors.forename: Sang-Yoon
authors.initials: SY
authors.lastname: Kim
authors.forename: Alistair C
authors.initials: AC
authors.lastname: Darby
authors.forename: Hans-Henrik
authors.initials: HH
authors.lastname: Fuxelius
authors.forename: Jun
authors.initials: J
authors.lastname: Yin
authors.forename: Ju Han
authors.initials: JH
authors.lastname: Kim
authors.forename: Jihun
authors.initials: J
authors.lastname: Kim
authors.forename: Sang Joo
authors.initials: SJ
authors.lastname: Lee
authors.forename: Young-Sang
authors.initials: YS
authors.lastname: Koh
authors.forename: Won-Jong
authors.initials: WJ
authors.lastname: Jang
authors.forename: Kyung-Hee
authors.initials: KH
authors.lastname: Park
authors.forename: Siv G E
authors.initials: SG
authors.lastname: Andersson
authors.forename: Myung-Sik
authors.initials: MS
authors.lastname: Choi
authors.forename: Ik-Sang
authors.initials: IS
authors.lastname: Kim
mesh_terms: D004251:DNA Transposable Elements; D020440:Gene Duplication; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D005810:Multigene Family; D012285:Orientia tsutsugamushi / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements