The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes.
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.
Cho
Nam-Hyuk
NH
Department of Microbiology and Immunology, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul 110-799, Republic of Korea.
Kim
Hang-Rae
HR
Lee
Jung-Hee
JH
Kim
Se-Yoon
SY
Kim
Jaejong
J
Cha
Sunho
S
Kim
Sang-Yoon
SY
Darby
Alistair C
AC
Fuxelius
Hans-Henrik
HH
Yin
Jun
J
Kim
Ju Han
JH
Kim
Jihun
J
Lee
Sang Joo
SJ
Koh
Young-Sang
YS
Jang
Won-Jong
WJ
Park
Kyung-Hee
KH
Andersson
Siv G E
SG
Choi
Myung-Sik
MS
Kim
Ik-Sang
IS
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
D004251:DNA Transposable Elements