Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

L. lactis Î?lmrCD and cholate-adapted L. lactis Î?lmrCDR

ABSTRACT: Transcriptome profiling of a L. lactis strain lacking the MDR transporter genes lmrCD and the same strain adapted to cholate was performed. As compared to the parental strain, the cholate-adapted strain showed 124 genes that were significantly differentially expressed more than 1.8-fold . These genes could be grouped into four major functional classes: i.e., genes involved in (i) cell envelope biogenesis; (ii) stress response and molecular chaperones; (iii) general metabolism and house-keeping function; and (iv) the chromosomally embedded sex-factor. Keywords: Mutant versus wild type comparison, stress response, cholate 1. WT1 L. lactis Î?lmrCD (labeled with Cy3) 2. WT2 L. lactis Î?lmrCD (labeled with Cy5) 3. WT4 L. lactis Î?lmrCD (labeled with Cy3) 4. WT5 L. lactis Î?lmrCD (labeled with Cy5) 5. M1 L. lactis Î?lmrCD(R) (labeled with Cy5) 6. M2 L. lactis Î?lmrCD(R)(labeled with Cy3) 7. M4 L. lactis Î?lmrCD(R) (labeled with Cy5) 8. M5 L. lactis Î?lmrCD(R) (labeled with Cy3) Hybridization schema: 1+5 (Slide 176631) 3+7 (Slide 176632) 2+8 (Slide 176633) 4+6 (Slide 176634)

ORGANISM(S): Lactococcus lactis

SUBMITTER: Anne Jong

PROVIDER: E-GEOD-10203 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The ABC-type multidrug resistance transporter LmrCD is responsible for an extrusion-based mechanism of bile acid resistance in Lactococcus lactis.

Zaidi Arsalan Haseeb AH Bakkes Patrick J PJ Lubelski Jacek J Agustiandari Herfita H Kuipers Oscar P OP Driessen Arnold J M AJ

Journal of bacteriology 20080912 22

Upon prolonged exposure to cholate and other toxic compounds, Lactococcus lactis develops a multidrug resistance phenotype that has been attributed to an elevated expression of the heterodimeric ABC-type multidrug transporter LmrCD. To investigate the molecular basis of bile acid resistance in L. lactis and to evaluate the contribution of efflux-based mechanisms in this process, the drug-sensitive L. lactis NZ9000 DeltalmrCD strain was challenged with cholate. A resistant strain was obtained tha ...[more]

PMID: 18790870

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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

L. lactis Î?lmrCD and cholate-adapted L. lactis Î?lmrCDR

Publications

The ABC-type multidrug resistance transporter LmrCD is responsible for an extrusion-based mechanism of bile acid resistance in Lactococcus lactis.

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