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    Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators (Finding Target Genes for TetR Family Regulators)

    Ahn, Sang Kyun, Cuthbertson, Leslie, Nodwell, Justin R
    2012, Vol.7(11), p.e50562 [Peer Reviewed Journal]
    PLoS
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    Title: Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators (Finding Target Genes for TetR Family Regulators)
    Author: Ahn, Sang Kyun; Cuthbertson, Leslie; Nodwell, Justin R
    Contributor: He, Bin (Editor)
    Subject: Research Article ; Biology ; Genetics And Genomics ; Microbiology ; Molecular Biology ; Computational Biology ; Biochemistry
    Description: T etR f amily transcriptional r egulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA . We explore predicted target gene product identity and intergenic separation to see which either correlates with a direct regulatory relationship. While intergenic separation is a critical factor in regulatory prediction the identity of the putative target gene product is not. Our data suggest that those TFRs that are
    Is part of: 2012, Vol.7(11), p.e50562
    Identifier: 1932-6203 (E-ISSN); 10.1371/journal.pone.0050562 (DOI)

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    Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators

    Ahn, Sang, Cuthbertson, Leslie, Nodwell, Justin
    PLoS One, Nov 2012, Vol.7(11), p.e50562 [Peer Reviewed Journal]
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    Title: Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators
    Author: Ahn, Sang; Cuthbertson, Leslie; Nodwell, Justin
    Subject: Pseudomonas Aeruginosa ; Ontario Canada ; Escherichia Coli ; Streptomyces ; Infectious Diseases ; Laboratories ; Pumps ; Pumps ; Product Differentiation ; Genes ; Efflux ; Biochemistry ; Genomes ; Biosynthesis ; Separation ; Regulators ; Bacteria ; Transcription ; Genomes ; E Coli
    Description: TetR family transcriptional regulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA. We explore predicted...
    Is part of: PLoS One, Nov 2012, Vol.7(11), p.e50562
    Identifier: 19326203 (E-ISSN); 10.1371/journal.pone.0050562 (DOI)

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    Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators

    Ahn, Sang Kyun, Cuthbertson, Leslie, Nodwell, Justin R
    PloS one, 2012, Vol.7(11), pp.e50562 [Peer Reviewed Journal]
    MEDLINE/PubMed (U.S. National Library of Medicine)
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    Title: Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators
    Author: Ahn, Sang Kyun; Cuthbertson, Leslie; Nodwell, Justin R
    Subject: Gene Expression Regulation, Bacterial ; Genomics ; Bacterial Proteins -- Metabolism ; Streptomyces Coelicolor -- Genetics ; Streptomyces Griseus -- Genetics ; Trans-Activators -- Metabolism
    Description: TetR family transcriptional regulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA. We explore predicted...
    Is part of: PloS one, 2012, Vol.7(11), pp.e50562
    Identifier: 1932-6203 (E-ISSN); 23226315 Version (PMID); 10.1371/journal.pone.0050562 (DOI)

    • Article
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    Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators

    Ahn, Sang Kyun, Cuthbertson, Leslie, Nodwell, Justin R
    PLoS ONE, 2012, Vol.7(11) [Peer Reviewed Journal]
    U.S. National Library of Medicine (NIH/NLM)
    Available
    More…
    Title: Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators
    Author: Ahn, Sang Kyun; Cuthbertson, Leslie; Nodwell, Justin R
    Contributor: He, Bin (editor)
    Subject: Research Article ; Biology
    Description: T etR f amily transcriptional r egulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA . We explore...
    Is part of: PLoS ONE, 2012, Vol.7(11)
    Identifier: 1932-6203 (E-ISSN); 10.1371/journal.pone.0050562 (DOI); 3511530 (PMCID); 23226315 (PMID)

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    Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators

    Sang Kyun Ahn, Leslie Cuthbertson, Justin R Nodwell
    PloS one, 01 January 2012, Vol.7(11), p.e50562 [Peer Reviewed Journal]
    Directory of Open Access Journals (DOAJ)
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    Title: Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators
    Author: Sang Kyun Ahn; Leslie Cuthbertson; Justin R Nodwell
    Subject: Sciences (General)
    Description: TetR family transcriptional regulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA. We explore...
    Is part of: PloS one, 01 January 2012, Vol.7(11), p.e50562
    Identifier: 1932-6203 (E-ISSN); 10.1371/journal.pone.0050562 (DOI)