Unknown,Transcriptomics,Genomics,Proteomics

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CodY of Streptococcus pneumoniae: link between nutritional gene regulation and virulence

ABSTRACT: CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillis subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY-mutant and examined the effect on gene and protein expression by microarray and 2D DIGE analysis. The pneumococcal CodY-regulon was found to consist predominantly of genes involved in amino acid metabolism, but also several other cellular processes, such as carbon metabolism and iron uptake. By means of electrophoretic mobility shift assays and DNA footprinting, we showed that most targets identified are under direct control of CodY. By mutating DNA predicted to represent the CodY-box based on the L. lactis consensus, we demonstrated that this sequence is indeed required for in vitro DNA-binding to target promoters. Similar to L. lactis, DNA-binding of CodY was enhanced in the presence of the branched chain amino acids isoleucine, leucine, and valine, and not by GTP. We observed in experimental mouse models that CodY is transcribed in the murine nasopharynx and lungs, and is specifically required for colonization. This finding was underscored by the diminished ability of the codY-mutant to adhere to nasopharyngeal cells in vitro. In conclusion, pneumococcal CodY predominantly regulates genes involved in amino acid metabolism and contributes to the early stages of infection, i.e. colonization of the nasopharynx. Keywords: codY CodY of Streptococcus pneumoniae: link between nutritional gene regulation and virulence

ORGANISM(S): Streptococcus pneumoniae TIGR4

SUBMITTER: Anne Jong

PROVIDER: E-GEOD-7350 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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CodY of Streptococcus pneumoniae: link between nutritional gene regulation and colonization.

Hendriksen Wouter T WT Bootsma Hester J HJ Estevão Silvia S Hoogenboezem Theo T de Jong Anne A de Groot Ronald R Kuipers Oscar P OP Hermans Peter W M PW

Journal of bacteriology 20071116 2

CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillus subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY mutant and examined the effect on gene and protein expression by microarray and two-dimensional differential gel electrophoresis analysis. The pneumococcal CodY regulon was found to consist predominantly of genes ...[more]

PMID: 18024519

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Project description:Background Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. In aCGH data, systematic errors are comparable to those occurring in transcriptome data. However, especially for microbes, an additional source of variation exists: differences in hybridization due to gene sequence divergence between the strains hybridized. Current normalization methods do not take this source of variation into consideration. Results We present Supervised Lowess, or S-Lowess, an application of the subset Lowess normalization method that does take difference in genomic content into account. The performance of S-Lowess was assessed on aCGH experiments in which differentially labeled genomic DNA fragments of Lactococcus lactis IL1403 and L. lactis MG1363 strains were hybridized to IL1403 microarrays. Since both genome sequences are known (they have only on average 85 % sequence identity), the success rate in detecting deletions in the MG1363 genome of different aCGH normalization methods can be compared. S-Lowess detects 97% of the deletions, whereas other aCGH normalization methods detect up to only 60% of the deletions. Conclusions S-Lowess removes systematic errors from dual-dye aCGH data in two steps: (i) determination of likely homologous genes (LHG); and (ii) estimation of correction factors for systematic errors from spots of LHG and subset Lowess normalization of the remaining spots using these correction factors. It is implemented in a user-friendly web-tool accessible from http://bioinformatics.biol.rug.nl/websoftware/s-lowess. We demonstrate that it outperforms existing normalization methods and maximizes the number of detectable genomic deletions or duplications from microbial aCGH data. Keywords: comparative genome hybridisation In this study, 4 aCGH comparisons (slides) between L. lactis MG1363 and L. lactis IL1403 were performed (including dye swap with biological replicates; see also supplementary materials). The resulting aCGH slide signals were normalized using the different 'likely homologous gene' (LHG) sets (see above) yielding ratios of signals of labelled DNA of MG1363 over those of IL1403. A maximum of 8 ratios per amplicon (gene) were obtained for the 4 hybridized slides (each with 2 replicate spots per amplicon). Only genes with at least 5 measurements were used in this study. The normalization methods evaluated in this study are: a) no normalization, b) total signal normalization, c) grid-based Lowess (implemented in PreP; f = 0.7) [GarcM-CM--a de la Nava, J et al. 2003. Bioinformatics 19:2328-2329], and d) S-Lowess using different subsets of conserved lactococcal genes (for details see above). Results with the MANOR R package (spatial normalization; standard parameters) [Neuvial P, et al. 2006. BMC Bioinformatics 7:264; Liva S, et al. 2006. Nucleic Acids Res 34:W477-W481] are shown in our supplementary materials.

Dataset Information

CodY of Streptococcus pneumoniae: link between nutritional gene regulation and virulence

Publications

CodY of Streptococcus pneumoniae: link between nutritional gene regulation and colonization.

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