RamA as a global regulator for gene expression in Salmonella Typhimurium
ABSTRACT: RamA, a 113-amino-acid regulatory protein, belongs to the AraC-XylS transcriptional activator family. Here, the network of genes regulated by RamA was investigated by determining changes in transcript profiles when ramA gene was knocked out from wild type LTL strain, which expresses ramA constitutively. Analysis used aerobic log-phase state RNA from S. Typhimurium strain LTL (ciprofloxacin MIC: 4 µg/ml) derived from S. Typhimurium LT2 by in vitro-induction using ciprofloxacin as control samples for comparison to the experimental samples taken from its mutant strain, LTLvramA with ramA-deletion. Six biological replicates were used for the experiment.Two replicates for each sample. One replicate per array.
Project description:DNA Microarray based comparison of M. tuberculosis and its isogenic delta-sigmaH mutant for an extended period of time, using a diamide-stress and removal strategy (post-diamide stress or PDS) Raw data has been requested of, but not provided by, the submitter. Two strains, M. tuberculosis vs delta-sigmaH mutant. At Pre-diamide (control), 0' 30' 60' 90' and 120' post-diamide stress, two biological replicates, six replicates per array
Project description:Proteus mirabilis is a primary cause of complicated urinary tract infections (UTI). Surprisingly, iron acquisition systems have been poorly characterized in this uropathogen despite the urinary tract being iron-limited. In this report the transcriptome of strain HI4320, cultured under iron limitation, was examined using microarray analysis. Of genes upregulated at least 2-fold, 45 were statistically significant and comprise 21 putative iron-regulated systems. Two of these systems, PMI0229-0239 and PMI2596-2605, are organized in operons and appear to encode siderophore biosynthesis genes. Five microarrays comparing P. mirabilis HI4320 cultured in LB broth to P. mirabilis cultured in LB broth + 15 uM Desferal (an iron chelator) were analyzed. All five arrays are biological replicates; arrays #2 and 4 are dye swaps.
Project description:Most sRNAs control the expression of target genes by interacting with their mRNA. The fvr1 (Francisella virulence RNA 1) gene is found in the IGR between FTL_0777 and FTL_0778 and its sequence does not overlap those of the flanking genes, indicating that its target(s) is located in trans. Base-pairing between a sRNA and target mRNA generally leads to changed translation and often the stability of the mRNA is affected as well. Therefore, to identify possible targets of Fvr1, we compared the transcriptomes of the LVS?fvr1(LVS, for Live Vaccine Strain) and LVS/pfvr1+ strains after growth in liquid broth.
Project description:The formation of Listeria monocytogenes biofilms contributes to persistent contamination in food processing facilities. A microarray comparison of L. monocytogenes between the transcriptome of the strong biofilm forming strain (Bfms) Scott A and the weak biofilm forming (Bfmw) strain F2365 was conducted to identify genes potentially involved in biofilm formation. Among 951 genes with significant difference in expression between the two strains, a GntR-family response regulator encoding gene (LMOf2365_0414), designated lbrA, was found to be highly expressed in Scott A relative to F2365. A Scott A lbrA-deletion mutant, designated AW3, formed biofilm to a much lesser extent as compared to the parent strain by a rapid attachment assay and scanning electron microscopy. Complementation with lbrA from Scott A restored the Bfms phenotype in the AW3 derivative. A second microarray assessment using the lbrA deletion mutant AW3 and the wild type Scott A revealed a total of 304 genes with expression significantly different between the two strains, indicating the potential regulatory role of LbrA in L. monocytogenes. A cloned copy of Scott A lbrA was unable to confer enhanced biofilm forming potential in F2365, suggesting that additional factors contributed to weak biofilm formation by F2365. Findings from the study may lead to new strategies to modulate biofilm formation. Two comparisons were performed between 1) strong biofilm former Listeria monocytogenes strain ScottA versus weak biofilm former Listeria monocytogenes strain F2365; 2) Listeria monocytogenes ScottA LbrA deletion mutant strain versus Listeria monocytogenes ScottA. Four replicates were loaded for the first comparison and two replicates were loaded for the second comparison.
Project description:The xprG gene encodes a putative transcriptional activator involved in the regulation of extracellular proteases in response to nutrient stress in Aspergillus nidulans. To investigate whether XprG is required for expression of other genes in response to carbon starvation, we used microarrays provided by the PFGRC. These experiments indicate that the expression of many genes, including the sterigmatocystin gene cluster and other secondary metabolism genes, genes involved in asexual and sexual development and genes induced during autolysis, is altered in an xprGdelta mutant. Many of these genes are known to be regulated in response to carbon starvation. The results indicate that XprG may play a major role in the response to carbon limitation. An xprG+ (wt) strain and xprGdelta gene knockout strain (ko) were compared after transfer to medium containing 1% glucose (C) or carbon-free medium (NC) for 16 hours. The effect of the two nutrient conditions on each strain were also investigated.
Project description:Light is a major environmental signal regulating many different biological processes. In Aspergillus nidulans light controls asexual and sexual development as well as the production of secondary metabolites. In order to get a global view of genes regulated during asexual development and of genes involved in other light-regulated biological processes, a genome-wide approach was undertaken. Total RNA was isolated from surface-grown, developmentally competent mycelia of the wild-type strain FGSC4 exposed to white light (11 W/m2) for 30 minutes or grown in the dark, labelled, and hybridized to a spotted microarray of A. nidulans.
Project description:RamA, a 113-amino-acid regulatory protein, belongs to the AraC-XylS transcriptional activator family. Here, the network of genes regulated by RamA was investigated by determining changes in transcript profiles when ramA gene was knocked out from wild type LTL strain, which expresses ramA constitutively. Overall design: Analysis used aerobic log-phase state RNA from S. Typhimurium strain LTL (ciprofloxacin MIC: 4 µg/ml) derived from S. Typhimurium LT2 by in vitro-induction using ciprofloxacin as control samples for comparison to the experimental samples taken from its mutant strain, LTLvramA with ramA-deletion. Six biological replicates were used for the experiment.Two replicates for each sample. One replicate per array.
Project description:Trypanosoma cruzi is an organism highly resistant to ionizing radiation. Following a dose of 500 Gy of gamma radiation, the fragmented genomic DNA is gradually reconstructed and the pattern of chromosomal bands is restored in less than 48 hours. Cell growth arrests after irradiation but, while DNA is completely fragmented, RNA maintains its integrity. In this work we compared the transcriptional profiles of irradiated and non-irradiated epimastigotes at different time points after irradiation using microarray. In total, 273 genes were differentially expressed; from these, 160 were up-regulated and 113 down-regulated. We found that genes with predicted functions are the most prevalent in the down-regulated gene category. Translation and protein metabolic processes, as well as generation of precursor of metabolites and energy pathways were affected. In contrast, the up-regulated category was mainly composed of obsolete sequences (which included some genes of the kinetoplast DNA), genes coding for hypothetical proteins, and Retrotransposon Hot Spot genes. Finally, the tyrosyl-DNA phosphodiesterase 1, a gene involved in double-strand DNA break repair process, was up-regulated. Our study demonstrated the peculiar response to ionizing radiation, raising questions about how this organism changes its gene expression to manage such a harmful stress. To evaluate the gamma radiation effect on T. cruzi epimastigote cells, two identical and independent experiments (biological replicates) were performed in triplicate. Each triplicate was composed of seven samples: cell culture growth control (not used in the microarray experiments), non-irradiated cells (used as reference sample in the microarray analysis), and five irradiated samples that had their RNA extracted immediately after irradiation (or i.a.i.), at 4, 24, 48, and 96 hours post-irradiation. Triplicates were pooled after the RNA extraction and before the purification/amplification steps. Each pool corresponding to one of the five time points was hybridized twice against the reference pool from each experiment, applying a reference time-course dye-swap design. Thus, four microarray slides for each time point were produced, two for each biological replicate, totaling 20 slides.
Project description:Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells. Two-condition experiment, Control Vs CIP treatment. Biological replicates: 3 control, One dye swap replicate. four samples and three biological replicate to study the response of S. coleicolor cells to ciprofloxacin