Unknown,Transcriptomics,Genomics,Proteomics

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Expression profile of crp-deficient Thermus thermophilus HB8 strain

ABSTRACT: We observed the expression profile of the total mRNA of crp (TTHA1437) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70 degC Three crp-deletion mutant T. thermophilus HB8 strains were each pre-cultured at 70 degC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70 degC. Cells were collected after 6 h and 8 h, and then crude RNA was extracted. The expression of mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

ORGANISM(S): Thermus thermophilus HB8

SUBMITTER: Yoshihiro Agari

PROVIDER: E-GEOD-21459 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We compared the expression profile of TTHA0118 deletion mutant strain of Thermus thermophils HB8 with that of wild-type. The mutant strain grown in minimum essential medium (CS medium) exhibited growth retardation. In early log phase, 29 genes were suppressed and 25 genes were activated for the mutant strain. The suppressed genes included genes of electron transport, and cell growth and division. The activated genes included genes of stress response. We suggested that these transcriptional alterations in the mutant cell were induced by the pAp accumulation and mononucleotides starvation. Keywords: cell type comparison Keywords: cell type comparison Wild-type and the mutant strains were precultured in rich medium (TT medium) for two times at 70 oC and then subcultured to minimum essential medium (CS medium). These cells were harvested at 7 × 10^8 cells/ml. Total RNA were extracted from each strain and used for the cDNA synthesis. For the biological replication, above experiments were performed four times independently. The cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer's instructions. The 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401 GeneChip (Affymetrix). The Probe Array was scanned with a GeneArray Scanner (Affymetrix), and then, the image data was scaled to the target intensity by one-step Tukey's biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix). The data analysis was performed by using GeneSpring GX (Agilent Tech.). The genes which had detection call of 'presence' more than 4 times from 8 samples were used for following analysis. The normalized intensities for the mutant strains were calculated by using the intensities for wild-type strains of each data set, and then, the average of these intensities were used. The genes which produced P value < 0.05 in the Student's t-test were extracted. Among them, the genes whose expression level was different more than 2 fold between two strains were considered as significant.

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Expression profile of crp-deficient Thermus thermophilus HB8 strain

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