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| Status |
Public on Feb 03, 2023 |
| Title |
The involvement of CdhR in Porphyromonas gingivalis during Nitric Oxide stress [microarray] |
| Platform organism |
Haemophilus influenzae |
| Sample organism |
Porphyromonas gingivalis W83 |
| Experiment type |
Expression profiling by array
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| Summary |
To understand the role of CdhR and its adjacent gene PG1236 in nitric oxide (NO) stress resistance, isogenic mutants P. gingivalis FLL457 (ΔPG1237::ermF), FLL458 (ΔPG1236::ermF) and FLL459 (ΔPG1236-37::ermF) were made by allelic exchange mutagenesis and their gene expression was studied under control and NO stress conditions. DNA microarray analysis of FLL457 showed that approximately 2% of the genes were up regulated and over 1% of the genes down regulated. Transcriptome analysis of FLL458 and FLL459 under NO stress showed similar modulation patterns in both mutants for a few genes. The PG1236-7 gene cluster seemed to be part of the same transcriptional unit that showed increased expression under NO stress. Recombinant CdhR showed binding activity to the predicted promoter regions of PG1459 and PG0495.
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| Overall design |
Fresh cultures of P. gingivalis strains (mutants and wild type) were grown from overnight cell cultures under anaerobic conditions at 37ºC in BHI broth. P. gingivalis strains were grown to early exponential phase (OD600:~0.3) in BHI broth under anaerobic conditions at 37ºC. At that time point, the bacteria cultures were stressed with Diethylamine (DEA) NONOate (15µl, 24mM stock concentration) for the NO stress studies and culture samples were taken 15min post-treatment with DEA NONOate. P. gingivalis W83 cultures and total RNA extracted from them using a total RNA isolation kit (Promega, WI). Additional DNase treatment was carried out using DNase kit (Ambion, Austin, TX). DNA microarray gene expression was carried out using Roche NimbleGen customer arrays (100910_CW_P_ging_W83_expr_HX12, Roche, IN) according to the standard NimbleGen procedure (NimbleGen Arrays User’s Guide: Gene Expression Analysis v5.1). cDNA was synthesized from the RNA samples using Transcriptor High Fidelity cDNA Synthesis kit (Roche, IN). Both RNA and cDNA quality were checked using Agilent Bioanalyzer and Agilent RNA 6000 Nano and DNA1000 chips. Differentially expressed genes were determined using fold-change (≥1.25) plus p (≤ 0.05) with FDR = 0.05.
***Please note that [1] raw data files have been lost and thus are not provided, [2] only the list of differentially-expressed genes is available and thus included as processed data*****
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| Contributor(s) |
Flether HM, Wang C, Mishra A, Dou Y |
| Citation(s) |
37134265 |
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| Submission date |
Jan 30, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Marie-Claire Boutrin |
| Organization name |
Oakwood University
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| Street address |
7000 Adventist Blvd NW
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| City |
Huntsville |
| ZIP/Postal code |
35896 |
| Country |
USA |
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| Platforms (1) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE224067 |
The involvement of CdhR in Porphyromonas gingivalis during Nitric Oxide stress |
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| Relations |
| BioProject |
PRJNA929507 |
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