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

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Published inJournal of Bacteriology Vol. 186; no. 17; pp. 5842 - 5855
Main Authors MCLEOD, Michael P, XIANG QIN, HAWES, Alicia C, SODERGREN, Erica, GILL, Rachel, HUME, Jennifer, MORGAN, Maggie, GUANGWEI FAN, AMIN, Anita G, GIBBS, Richard A, CHAO HONG, YU, Xue-Jie, KARPATHY, Sandor E, WALKER, David H, WEINSTOCK, George M, GIOIA, Jason, HIGHLANDER, Sarah K, FOX, George E, MCNEILL, Thomas Z, HUAIYANG JIANG, MUZNY, Donna, JACOB, Leni S
Format Journal Article
LanguageEnglish
Published Washington, DC American Society for Microbiology 01.09.2004
Subjects
Bacteria
Bacterial proteins
Bacteriology
Biological and medical sciences
Chromosome Inversion
DNA, Bacterial - chemistry
DNA, Bacterial - isolation & purification
Electron Transport Complex IV - genetics
Frameshifting, Ribosomal
Fundamental and applied biological sciences. Psychology
Gene Expression Regulation, Bacterial
Gene Rearrangement
Genes, Bacterial
Genes, rRNA
Genome, Bacterial
Genomics
Genomics and Proteomics
Microbiology
Miscellaneous
Molecular Sequence Data
Pseudogenes
Rickettsia - genetics
Rickettsia conorii
Rickettsia conorii - genetics
Rickettsia prowazekii
Rickettsia typhi
Rickettsia typhi - genetics
RNA, Transfer - genetics
RNA, Untranslated - genetics
Sequence Analysis, DNA
Sequence Homology
Synteny
Rickettsiales
Microbiology
Nucleotide sequence
Bacteria
Rickettsieae
Rickettsia typhi
Rickettsiaceae
Bacteriology
Online AccessGet full text

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Abstract Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue JB About JB Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy JB RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0021-9193 Online ISSN: 1098-5530 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to JB .asm.org, visit: JB       
AbstractList Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue JB About JB Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy JB RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0021-9193 Online ISSN: 1098-5530 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to JB .asm.org, visit: JB       
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.
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.
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. [PUBLICATION 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.
Author Chao Hong
Alicia C. Hawes
Sandor E. Karpathy
Thomas Z. McNeill
Rachel Gill
Michael P. McLeod
Anita G. Amin
Leni S. Jacob
Xiang Qin
Jason Gioia
George M. Weinstock
Jennifer Hume
Huaiyang Jiang
Xue-jie Yu
David H. Walker
Guangwei Fan
Maggie Morgan
Richard A. Gibbs
Erica Sodergren
Sarah K. Highlander
George E. Fox
Donna Muzny
AuthorAffiliation 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, Texas 5
AuthorAffiliation_xml – name: 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, Texas 5
Author_xml – sequence: 1
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  surname: MCLEOD
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  organization: Human Genome Sequencing Center, University of Houston, United States
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  fullname: HAWES, Alicia C
  organization: Human Genome Sequencing Center, University of Houston, United States
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  surname: SODERGREN
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  organization: Human Genome Sequencing Center, University of Houston, United States
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  surname: GILL
  fullname: GILL, Rachel
  organization: Human Genome Sequencing Center, University of Houston, United States
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  organization: Human Genome Sequencing Center, University of Houston, United States
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  organization: Human Genome Sequencing Center, University of Houston, United States
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  surname: GIBBS
  fullname: GIBBS, Richard A
  organization: Human Genome Sequencing Center, University of Houston, United States
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  surname: CHAO HONG
  fullname: CHAO HONG
  organization: Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States
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  surname: YU
  fullname: YU, Xue-Jie
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  givenname: Sandor E
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  fullname: KARPATHY, Sandor E
  organization: Human Genome Sequencing Center, University of Houston, United States
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  fullname: WALKER, David H
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  surname: MCNEILL
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  organization: Human Genome Sequencing Center, University of Houston, United States
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  surname: HUAIYANG JIANG
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  organization: Human Genome Sequencing Center, University of Houston, United States
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  surname: MUZNY
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  givenname: Leni S
  surname: JACOB
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  organization: Human Genome Sequencing Center, University of Houston, United States
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https://www.ncbi.nlm.nih.gov/pubmed/15317790$$D View this record in MEDLINE/PubMed
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Issue 17
Keywords Rickettsiales
Microbiology
Nucleotide sequence
Bacteria
Rickettsieae
Rickettsia typhi
Rickettsiaceae
Bacteriology
Language English
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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@bcm.tmc.edu.
M.P.M. and X.Q. contributed equally to this study.
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Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate...
ABSTRACT Rickettsia typhi , the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and...
Rickettsia typhi , the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate...
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SourceType Open Access Repository
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StartPage 5842
SubjectTerms Bacteria
Bacterial proteins
Bacteriology
Biological and medical sciences
Chromosome Inversion
DNA, Bacterial - chemistry
DNA, Bacterial - isolation & purification
Electron Transport Complex IV - genetics
Frameshifting, Ribosomal
Fundamental and applied biological sciences. Psychology
Gene Expression Regulation, Bacterial
Gene Rearrangement
Genes, Bacterial
Genes, rRNA
Genome, Bacterial
Genomics
Genomics and Proteomics
Microbiology
Miscellaneous
Molecular Sequence Data
Pseudogenes
Rickettsia - genetics
Rickettsia conorii
Rickettsia conorii - genetics
Rickettsia prowazekii
Rickettsia typhi
Rickettsia typhi - genetics
RNA, Transfer - genetics
RNA, Untranslated - genetics
Sequence Analysis, DNA
Sequence Homology
Synteny
Title Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae
URI http://jb.asm.org/content/186/17/5842.abstract
https://www.ncbi.nlm.nih.gov/pubmed/15317790
https://www.proquest.com/docview/227059421
https://search.proquest.com/docview/18019323
https://pubmed.ncbi.nlm.nih.gov/PMC516817
Volume 186
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