Streptococcus mutans UA159 with or without 8.4% oxygen vs. nox mutant strain. pH5
Ontology highlight
ABSTRACT:
ORGANISM(S): Streptococcus mutans UA159
SUBMITTER: Roberta Faustoferri
PROVIDER: E-GEOD-56118 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional analysis of the effects of sugar source in S. mutans RNA was extracted from 4 replicate samples of S. mutans UA159, UA159 grown in glucose or maltose in continuous culture to steady-state pH values of 7 or 5. RNA was labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.
2014-06-01 | E-GEOD-55952 | biostudies-arrayexpress
Project description:Transcriptional analysis of the regulator FabT in S. mutans RNA was extracted from 4 replicate samples of S. mutans UA159 and MU1591 (M-bM-^HM-^FfabT) grown in continuous culture to steady-state pH values of 7 and 5. RNA was labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.
2012-05-31 | E-GEOD-36960 | biostudies-arrayexpress
Project description:Transcriptional analysis of glucose shock vs. steady-state growth in the parent strain and an acid sensitive mutant strain of S. mutans RNA was extracted from 4 replicate samples of S. mutans UA159 and UR117 (fabM mutant strain) grown in continuous culture to a steady-state pH value of 7. The cultures were exposed to a glucose shock (200mM) and samples were collected upon achieving culture pH value of 5.5. pH control was re-established and cultures were allowed to grow to a steady-state pH value of 5 (for UA159) and 5.5 (for fabM mutant). RNA was labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.
2015-02-15 | E-GEOD-64236 | biostudies-arrayexpress
Project description:Transcriptional analysis of the effects of oxygen concentraion in S. mutans RNA was extracted from 3 or 4 replicate samples of S. mutans UA159, UA159 grown in 8.4 % oxygen concentration and MU1020 (M-bM-^HM-^Fnox) grown in continuous culture to steady-state pH values of 7. RNA was labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.
2012-10-04 | E-GEOD-38803 | biostudies-arrayexpress
Project description:Transcriptional profiling to investigate the regulatory roles of SpxA and SpxB of S. mutans. RNA was extracted from four replicate samples of each strain of interest (spxA mutant, spxB mutant, spxAB double-mutant, UA159 wild type) and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.
2010-05-16 | E-GEOD-19656 | biostudies-arrayexpress
Project description:Transcriptional profiling to investigate the roles of ClpP and ClpX of S. mutans RNA was extracted from four replicate samples of each strain of interest and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.
2011-06-10 | E-GEOD-29871 | biostudies-arrayexpress
Project description:Transcriptional profiling to investigate the response of Streptococcus mutans biofilms to starch and sucrose. RNA was extracted and purified from four replicate samples of each biofilm sample of interest and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.
2010-05-18 | E-GEOD-21872 | biostudies-arrayexpress
Project description:Transcriptional profiling to investigate the response of Streptococcus mutans biofilms to starch and sucrose at distinct stages of biofilm development. RNA was extracted and purified from four replicate samples of each biofilm sample of interest and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.
2010-05-15 | E-GEOD-21831 | biostudies-arrayexpress
Project description:In consideration of the fact that BrpA expression is at its maximum during early-exponential phase as shown by Northern blotting and reporter gene fusion assays, we carried out a DNA microarray analysis using total RNA from early exponential phase cultures (OD600nm=0.3). It was found that 92 genes were up-regulated and 90 down-regulated in TW14D by a factor of at least 1.5-fold (p ≤ 0.001). At a level of P<0.01, 176 additional genes were found to be differentially expressed in TW14D, with 77 up- and 90 down-regulated. Based on the description and putative functions of the genes identified at the significance level of P<0.001, BrpA-deficiency affects almost every aspect of the cellular physiology as well as virulence properties, including amino acid biosynthesis, carbohydrates and energy metabolism, nucleic acids and DNA metabolism, transcriptional regulation, ABC transporters, molecular chaperones and other cellular processes, and hypothetical and conserved hypothetical proteins. The breadth of impact of BrpA-deficiency on the transcriptional profile of the deficient mutant is similar to what was observed previously with mid-exponential phase cells. However, comparison of the two transcriptional profiles revealed that only a small number of genes were consistently up- or down-regulated in both early- and mid-exponential phase cultures, which include recA (for recombinant protein RecA), gtfD (for glucosyltransferase D), wapA (for surface-associated protein WapA), groEL (for molecular chaperone GroEL) and sod (for Mn-dependent superoxide dismutase SOD). In addition, the magnitude of alterations in gene expression was also more dramatic in cells of the early-exponential phase, when compared to that in the mid-exponential phase cultures. Of the genes altered as a result of BrpA-deficiency in early-exponential phase cultures, several were found to encode proteins with potential roles in peptidoglycan biosynthesis. Among them are SMU.246 for a phospho-MurNAc-pentapeptide-transferase (RgpG), SMU.549 for an undecaprenyl-PP-MurNAc-pentapeptide-UDP-GlcNAc transferase (MurG), SMU.599 for a D-alanine-D-alanine ligase (DdlA), and SMU.1677 for a UDP-MurNAc-tripeptide synthetase (MurE). Besides, several genes encoding components of the Sec translocase were also found altered in TW14D. These included secA, secE and secY encoding the ATP-dependent motor of the translocation machinery, SecA, and the translocon pore components, SecE and SecY, respectively. Both secA and secE were down-regulated by more than 2-fold, while secY was up-regulated by more than 2-fold. Transcriptional profiling of S. mutans was done using a spotted array (version II) obtained from TIGR (JCVI). The wild-type UA159 and its BrpA-deficient mutant (TW14D) were grown in plain BHI broth until early phase OD=0.3. Four replicates each. A common reference (mid-exponential phase wild-type UA159) was used.
2012-01-26 | E-GEOD-35349 | biostudies-arrayexpress
Project description:Global transcriptional analysis of acid-inducible genes in Streptococcus mutans: multiple two-component systems involved in acid adaptation pH is a major environmental factor that regulates gene expression in many bacteria. Streptococcus mutans in dental biofilms is regularly exposed to cycles of acidic pH during the ingestion of fermentable dietary carbohydrates. The ability of S. mutans to tolerate low pH is crucial for its virulence and the pathogenesis in dental caries. To better understand its acid tolerance mechanisms, we used DNA microarray to perform genome-wide transcriptional analysis of S. mutans in response to acidic pH. The results showed that adaptation of S. mutans to pH 5.5 for 2 hrs induced differential expression of nearly 14% of genes in the genome, including 169 up-regulated genes and 108 down-regulated genes, largely categorized into six groups. Especially, we found that the genes encoding multiple two-component systems, including CiaHR, LevSR, LiaSR, ScnKR, HK/RR07 and ComDE, were up-regulated during acid adaptation. These findings were further confirmed by real time qRT-PCR and phenotypic assays of the gene deletion mutants. The results support that the multiple two-component systems are required for S. mutans to orchestrate its signal transduction networks for optimal adaptation to acidic pH. Total RNAs were isolated from S. mutans UA159 cells (0.6 at OD600) grown in a TYG broth (3% tryptone, 0.3% yeast extract and 20 mM glucose) at either pH 5.5 or pH 7.5. The RNAs were treated with RNase-free DNase 1 and purified by Qiagen RNeasy mini columns. The purified RNAs were used to generate cDNA probes by an indirect labeling method based on the protocol from TIGR. The cDNAs were coupled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen). The labeled cDNA probes from three different cultures of UA159 were hybridized to the S. mutans microarray slides obtained from PFGRC (http://pfgrc.tigr.org). Array hybridization was conducted using a protocol from the PFGRC with minor modification. After hybridization, washes and dried, the array slides were scanned by ScanArray 5000XL Reader (Perkin Elmer, Boston, MA). After the array slides were scanned, the resulting images were loaded into TIGR Spotfinder software (http://www.tigr.org/software/) and overlaid. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, and the intensity values of each spot were determined. Signal intensities of individual channels from an array slide were averaged and normalized using an array data analysis software (MIDAS) by using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis. A t-test was used to determine the consistency of ratios across replicate hybridizations. Only genes whose ratios were ⥠2-fold changes (either increase or decrease) with 99% confidence interval (P ⤠0.01) were considered statistically significant.
2010-05-22 | E-GEOD-15125 | biostudies-arrayexpress