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Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics.

Yoder-Himes DR, Konstantinidis KT, Tiedje JM - PLoS ONE (2010)

Bottom Line: Conservation of these induced genes was established using the 11 available Bcc genome sequences to indicate whether potential therapeutic targets would be species-wide.Comparative transcriptomics is a useful way to identify new potential virulence factors and therapeutic targets for pathogenic bacteria.We identified eight genes induced under CF conditions that were also conserved in the Bcc and may constitute particularly attractive therapeutic targets due to their signal sequence, predicted cellular location, and homology to known therapeutic targets.

View Article: PubMed Central - PubMed

Affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America.

ABSTRACT

Background: Burkholderia cenocepacia is an endemic soil dweller and emerging opportunistic pathogen in patients with cystic fibrosis (CF). The identification of virulence factors and potential therapeutic targets has been hampered by the genomic diversity within the species as many factors are not shared among the pathogenic members of the species.

Methodology/principal findings: In this study, global identification of putative virulence factors was performed by analyzing the transcriptome of two related strains of B. cenocepacia (one clinical, one environmental) under conditions mimicking cystic fibrosis sputum versus soil. Soil is a natural reservoir for this species; hence, genes induced under CF conditions relative to soil may represent adaptations that have occurred in clinical strains. Under CF conditions, several genes encoding proteins thought to be involved in virulence were induced and many new ones were identified. Our analysis, in combination with previous studies, reveals 458 strain-specific genes, 126 clinical-isolate-specific, and at least four species-specific genes that are induced under CF conditions. The chromosomal distribution of the induced genes was disproportionate to the size of the chromosome as genes expressed under soil conditions by both strains were more frequent on the second chromosome and those differentially regulated between strains were more frequent on the third chromosome. Conservation of these induced genes was established using the 11 available Bcc genome sequences to indicate whether potential therapeutic targets would be species-wide.

Conclusions/significance: Comparative transcriptomics is a useful way to identify new potential virulence factors and therapeutic targets for pathogenic bacteria. We identified eight genes induced under CF conditions that were also conserved in the Bcc and may constitute particularly attractive therapeutic targets due to their signal sequence, predicted cellular location, and homology to known therapeutic targets.

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Related in: MedlinePlus

Quantitative real-time PCR verification of microarray data.Twenty-two genes were tested for gene expression ratios and plotted as ratios (either J2315 CF/SE or J2315/HI2424). Error bars correspond to a single standard deviation of the data.
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pone-0008724-g005: Quantitative real-time PCR verification of microarray data.Twenty-two genes were tested for gene expression ratios and plotted as ratios (either J2315 CF/SE or J2315/HI2424). Error bars correspond to a single standard deviation of the data.

Mentions: To verify the overexpression ratios observed in the microarray data, qRT-PCR was performed on 21 unlinked chromosomal genes. The genes were chosen based on their putative functions and overexpression patterns in J2315 under CF conditions and include, ClpB protease-associated ATPase, curli production protein, ecotin biosynthesis protein, a multidrug resistance transport protein, phenazine biosynthesis protein; type-1 fimbrial protein, exported heme utilization protein, N-acylhomoserine lactone synthase, general secretory pathway protein F, TraE conjugative transfer protein. Additionally, genes induced in HI2424 (CheA signal transduction histidine kinase, chaperonin Cpn10, flagellar motor switch protein, host factor Hfq, phenylacetate degradation enoyl-CoA hydratase, and urease accessory protein D) or in J2315 under SE conditions (a flp pilus subunit, a lectin, nitrite reductase, polyhydroxybutyrate depolymerase, putrescine permease, spermidine synthase) were also analyzed. Overexpression ratios were statistically consistent with microarray ratios for the 13 of the 20 genes tested (Fig. 5). In the remaining 7 genes, the overall trend of gene expression was similar for both microarray and qRT-PCR ratios but the extent of induction differed up to 5-fold. These results indicate that the microarray data reflects the transcript ratios for the majority of genes.


Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics.

Yoder-Himes DR, Konstantinidis KT, Tiedje JM - PLoS ONE (2010)

Quantitative real-time PCR verification of microarray data.Twenty-two genes were tested for gene expression ratios and plotted as ratios (either J2315 CF/SE or J2315/HI2424). Error bars correspond to a single standard deviation of the data.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2806911&req=5

pone-0008724-g005: Quantitative real-time PCR verification of microarray data.Twenty-two genes were tested for gene expression ratios and plotted as ratios (either J2315 CF/SE or J2315/HI2424). Error bars correspond to a single standard deviation of the data.
Mentions: To verify the overexpression ratios observed in the microarray data, qRT-PCR was performed on 21 unlinked chromosomal genes. The genes were chosen based on their putative functions and overexpression patterns in J2315 under CF conditions and include, ClpB protease-associated ATPase, curli production protein, ecotin biosynthesis protein, a multidrug resistance transport protein, phenazine biosynthesis protein; type-1 fimbrial protein, exported heme utilization protein, N-acylhomoserine lactone synthase, general secretory pathway protein F, TraE conjugative transfer protein. Additionally, genes induced in HI2424 (CheA signal transduction histidine kinase, chaperonin Cpn10, flagellar motor switch protein, host factor Hfq, phenylacetate degradation enoyl-CoA hydratase, and urease accessory protein D) or in J2315 under SE conditions (a flp pilus subunit, a lectin, nitrite reductase, polyhydroxybutyrate depolymerase, putrescine permease, spermidine synthase) were also analyzed. Overexpression ratios were statistically consistent with microarray ratios for the 13 of the 20 genes tested (Fig. 5). In the remaining 7 genes, the overall trend of gene expression was similar for both microarray and qRT-PCR ratios but the extent of induction differed up to 5-fold. These results indicate that the microarray data reflects the transcript ratios for the majority of genes.

Bottom Line: Conservation of these induced genes was established using the 11 available Bcc genome sequences to indicate whether potential therapeutic targets would be species-wide.Comparative transcriptomics is a useful way to identify new potential virulence factors and therapeutic targets for pathogenic bacteria.We identified eight genes induced under CF conditions that were also conserved in the Bcc and may constitute particularly attractive therapeutic targets due to their signal sequence, predicted cellular location, and homology to known therapeutic targets.

View Article: PubMed Central - PubMed

Affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America.

ABSTRACT

Background: Burkholderia cenocepacia is an endemic soil dweller and emerging opportunistic pathogen in patients with cystic fibrosis (CF). The identification of virulence factors and potential therapeutic targets has been hampered by the genomic diversity within the species as many factors are not shared among the pathogenic members of the species.

Methodology/principal findings: In this study, global identification of putative virulence factors was performed by analyzing the transcriptome of two related strains of B. cenocepacia (one clinical, one environmental) under conditions mimicking cystic fibrosis sputum versus soil. Soil is a natural reservoir for this species; hence, genes induced under CF conditions relative to soil may represent adaptations that have occurred in clinical strains. Under CF conditions, several genes encoding proteins thought to be involved in virulence were induced and many new ones were identified. Our analysis, in combination with previous studies, reveals 458 strain-specific genes, 126 clinical-isolate-specific, and at least four species-specific genes that are induced under CF conditions. The chromosomal distribution of the induced genes was disproportionate to the size of the chromosome as genes expressed under soil conditions by both strains were more frequent on the second chromosome and those differentially regulated between strains were more frequent on the third chromosome. Conservation of these induced genes was established using the 11 available Bcc genome sequences to indicate whether potential therapeutic targets would be species-wide.

Conclusions/significance: Comparative transcriptomics is a useful way to identify new potential virulence factors and therapeutic targets for pathogenic bacteria. We identified eight genes induced under CF conditions that were also conserved in the Bcc and may constitute particularly attractive therapeutic targets due to their signal sequence, predicted cellular location, and homology to known therapeutic targets.

Show MeSH
Related in: MedlinePlus