Complete genome sequence of francisella tularensis subspecies holarctica FTNF002-00

Ravi D. Barabote, Gary Xie, Thomas S. Brettin, Steven Heye Hinrichs, Paul D Fey, Justin J. Jay, Jeniffer L. Engle, Shubhada D. Godbole, Jyothi M. Noronha, Richard H. Scheuermann, Liwel W. Zhou, Christine Lion, Michael P. Dempsey

Research output: Contribution to journalArticle

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Abstract

Francisella tularensis subspecies holarctica FTNF002-00 strain was originally obtained from the first known clinical case of bacteremic F. tularensis pneumonia in Southern Europe isolated from an immunocompetent individual. The FTNF002-00 complete genome contains the RD23 deletion and represents a type strain for a clonal population from the first epidemic tularemia outbreak in Spain between 1997-1998. Here, we present the complete sequence analysis of the FTNF002-00 genome. The complete genome sequence of FTNF002-00 revealed several large as well as small genomic differences with respect to two other published complete genome sequences of F. tularensis subsp. holarctica strains, LVS and OSU18. The FTNF002-00 genome shares >99.9% sequence similarity with LVS and OSU18, and is also ∼5 MB smaller by comparison. The overall organization of the FTNF002-00 genome is remarkably identical to those of LVS and OSU18, except for a single 3.9 kb inversion in FTNF002-00. Twelve regions of difference ranging from 0.1-1.5 kb and forty-two small insertions and deletions were identified in a comparative analysis of FTNF002-00, LVS, and OSU18 genomes. Two small deletions appear to inactivate two genes in FTNF002-00 causing them to become pseudogenes; the intact genes encode a protein of unknown function and a drug:H+ antiporter. In addition, we identified ninety-nine proteins in FTNF002-00 containing amino acid mutations compared to LVS and OSU18. Several non-conserved amino acid replacements were identified, one of which occurs in the virulence-associated intracellular growth locus subunit D protein. Many of these changes in FTNF002-00 are likely the consequence of direct selection that increases the fitness of this subsp. holarctica clone within its endemic population. Our complete genome sequence analyses lay the foundation for experimental testing of these possibilities.

Original languageEnglish (US)
Article numbere7041
JournalPloS one
Volume4
Issue number9
DOIs
StatePublished - Sep 16 2009

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Francisella tularensis
Genes
Genome
genome
Sequence Analysis
Francisella tularensis subsp. holarctica
tularemia
Antiporters
Tularemia
Amino Acids
antiporters
Pseudogenes
amino acids
proteins
pseudogenes
Southern European region
Protein Subunits
Proteins
Spain
pneumonia

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Complete genome sequence of francisella tularensis subspecies holarctica FTNF002-00. / Barabote, Ravi D.; Xie, Gary; Brettin, Thomas S.; Hinrichs, Steven Heye; Fey, Paul D; Jay, Justin J.; Engle, Jeniffer L.; Godbole, Shubhada D.; Noronha, Jyothi M.; Scheuermann, Richard H.; Zhou, Liwel W.; Lion, Christine; Dempsey, Michael P.

In: PloS one, Vol. 4, No. 9, e7041, 16.09.2009.

Research output: Contribution to journalArticle

Barabote, RD, Xie, G, Brettin, TS, Hinrichs, SH, Fey, PD, Jay, JJ, Engle, JL, Godbole, SD, Noronha, JM, Scheuermann, RH, Zhou, LW, Lion, C & Dempsey, MP 2009, 'Complete genome sequence of francisella tularensis subspecies holarctica FTNF002-00', PloS one, vol. 4, no. 9, e7041. https://doi.org/10.1371/journal.pone.0007041
Barabote, Ravi D. ; Xie, Gary ; Brettin, Thomas S. ; Hinrichs, Steven Heye ; Fey, Paul D ; Jay, Justin J. ; Engle, Jeniffer L. ; Godbole, Shubhada D. ; Noronha, Jyothi M. ; Scheuermann, Richard H. ; Zhou, Liwel W. ; Lion, Christine ; Dempsey, Michael P. / Complete genome sequence of francisella tularensis subspecies holarctica FTNF002-00. In: PloS one. 2009 ; Vol. 4, No. 9.
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abstract = "Francisella tularensis subspecies holarctica FTNF002-00 strain was originally obtained from the first known clinical case of bacteremic F. tularensis pneumonia in Southern Europe isolated from an immunocompetent individual. The FTNF002-00 complete genome contains the RD23 deletion and represents a type strain for a clonal population from the first epidemic tularemia outbreak in Spain between 1997-1998. Here, we present the complete sequence analysis of the FTNF002-00 genome. The complete genome sequence of FTNF002-00 revealed several large as well as small genomic differences with respect to two other published complete genome sequences of F. tularensis subsp. holarctica strains, LVS and OSU18. The FTNF002-00 genome shares >99.9{\%} sequence similarity with LVS and OSU18, and is also ∼5 MB smaller by comparison. The overall organization of the FTNF002-00 genome is remarkably identical to those of LVS and OSU18, except for a single 3.9 kb inversion in FTNF002-00. Twelve regions of difference ranging from 0.1-1.5 kb and forty-two small insertions and deletions were identified in a comparative analysis of FTNF002-00, LVS, and OSU18 genomes. Two small deletions appear to inactivate two genes in FTNF002-00 causing them to become pseudogenes; the intact genes encode a protein of unknown function and a drug:H+ antiporter. In addition, we identified ninety-nine proteins in FTNF002-00 containing amino acid mutations compared to LVS and OSU18. Several non-conserved amino acid replacements were identified, one of which occurs in the virulence-associated intracellular growth locus subunit D protein. Many of these changes in FTNF002-00 are likely the consequence of direct selection that increases the fitness of this subsp. holarctica clone within its endemic population. Our complete genome sequence analyses lay the foundation for experimental testing of these possibilities.",
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