Genomic islands from five strains of Burkholderia pseudomallei

Apichai Tuanyok, Benjamin Leadem, Raymond Auerbach, Stephen Beckstrom-Sternberg, James Beckstrom-Sternberg, Mark Mayo, Vanaporn Wuthiekanun, Thomas Brettin, William Nierman, Sharon J Peacock, Bart Currie, David M Wagner, Paul S Keim

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    Background: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3? end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species. � 2008 Tuanyok et al; licensee BioMed Central Ltd.
    Original languageEnglish
    Pages (from-to)1-14
    Number of pages14
    JournalBMC Genomics
    Volume9
    Publication statusPublished - 2008

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    Burkholderia pseudomallei
    Genomic Islands
    Transfer RNA
    Melioidosis
    Interspersed Repetitive Sequences
    Terminology
    Genetic Recombination
    Genes
    Genome
    Morbidity

    Cite this

    Tuanyok, A., Leadem, B., Auerbach, R., Beckstrom-Sternberg, S., Beckstrom-Sternberg, J., Mayo, M., ... Keim, P. S. (2008). Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics, 9, 1-14.
    Tuanyok, Apichai ; Leadem, Benjamin ; Auerbach, Raymond ; Beckstrom-Sternberg, Stephen ; Beckstrom-Sternberg, James ; Mayo, Mark ; Wuthiekanun, Vanaporn ; Brettin, Thomas ; Nierman, William ; Peacock, Sharon J ; Currie, Bart ; Wagner, David M ; Keim, Paul S. / Genomic islands from five strains of Burkholderia pseudomallei. In: BMC Genomics. 2008 ; Vol. 9. pp. 1-14.
    @article{1517e7f8ce8e40d8a962d2c1e2fb896d,
    title = "Genomic islands from five strains of Burkholderia pseudomallei",
    abstract = "Background: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3? end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term {"}tRNA-mediated site-specific recombination{"} (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species. � 2008 Tuanyok et al; licensee BioMed Central Ltd.",
    keywords = "transfer RNA, 3' untranslated region, article, bacterial genetics, bacterial genome, bacterial strain, Burkholderia pseudomallei, controlled study, gene locus, gene sequence, genetic recombination, genetic variability, genomic island, nonhuman, nucleotide sequence, strain difference, Burkholderia mallei, genetics, horizontal gene transfer, nomenclature, Bacteria (microorganisms), Gene Transfer, Horizontal, Genetic Variation, Genomic Islands, RNA, Transfer, Terminology as Topic",
    author = "Apichai Tuanyok and Benjamin Leadem and Raymond Auerbach and Stephen Beckstrom-Sternberg and James Beckstrom-Sternberg and Mark Mayo and Vanaporn Wuthiekanun and Thomas Brettin and William Nierman and Peacock, {Sharon J} and Bart Currie and Wagner, {David M} and Keim, {Paul S}",
    year = "2008",
    language = "English",
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    pages = "1--14",
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    Tuanyok, A, Leadem, B, Auerbach, R, Beckstrom-Sternberg, S, Beckstrom-Sternberg, J, Mayo, M, Wuthiekanun, V, Brettin, T, Nierman, W, Peacock, SJ, Currie, B, Wagner, DM & Keim, PS 2008, 'Genomic islands from five strains of Burkholderia pseudomallei', BMC Genomics, vol. 9, pp. 1-14.

    Genomic islands from five strains of Burkholderia pseudomallei. / Tuanyok, Apichai; Leadem, Benjamin; Auerbach, Raymond; Beckstrom-Sternberg, Stephen; Beckstrom-Sternberg, James; Mayo, Mark; Wuthiekanun, Vanaporn; Brettin, Thomas; Nierman, William; Peacock, Sharon J; Currie, Bart; Wagner, David M; Keim, Paul S.

    In: BMC Genomics, Vol. 9, 2008, p. 1-14.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Genomic islands from five strains of Burkholderia pseudomallei

    AU - Tuanyok, Apichai

    AU - Leadem, Benjamin

    AU - Auerbach, Raymond

    AU - Beckstrom-Sternberg, Stephen

    AU - Beckstrom-Sternberg, James

    AU - Mayo, Mark

    AU - Wuthiekanun, Vanaporn

    AU - Brettin, Thomas

    AU - Nierman, William

    AU - Peacock, Sharon J

    AU - Currie, Bart

    AU - Wagner, David M

    AU - Keim, Paul S

    PY - 2008

    Y1 - 2008

    N2 - Background: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3? end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species. � 2008 Tuanyok et al; licensee BioMed Central Ltd.

    AB - Background: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species. Results: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3? end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described. Conclusion: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species. � 2008 Tuanyok et al; licensee BioMed Central Ltd.

    KW - transfer RNA

    KW - 3' untranslated region

    KW - article

    KW - bacterial genetics

    KW - bacterial genome

    KW - bacterial strain

    KW - Burkholderia pseudomallei

    KW - controlled study

    KW - gene locus

    KW - gene sequence

    KW - genetic recombination

    KW - genetic variability

    KW - genomic island

    KW - nonhuman

    KW - nucleotide sequence

    KW - strain difference

    KW - Burkholderia mallei

    KW - genetics

    KW - horizontal gene transfer

    KW - nomenclature

    KW - Bacteria (microorganisms)

    KW - Gene Transfer, Horizontal

    KW - Genetic Variation

    KW - Genomic Islands

    KW - RNA, Transfer

    KW - Terminology as Topic

    M3 - Article

    VL - 9

    SP - 1

    EP - 14

    JO - BMC Genomics

    JF - BMC Genomics

    SN - 1471-2164

    ER -

    Tuanyok A, Leadem B, Auerbach R, Beckstrom-Sternberg S, Beckstrom-Sternberg J, Mayo M et al. Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics. 2008;9:1-14.