Peroxide stress in Sigma54 mutant and Wt
Ontology highlight
ABSTRACT:
ORGANISM(S): Lactiplantibacillus plantarum WCFS1 Lactiplantibacillus plantarum
PROVIDER: GSE11351 | GEO | 2008/05/08
SECONDARY ACCESSION(S): PRJNA106569
REPOSITORIES: GEO
Similar Datasets
Project description:Analyses of the Wild type and the sigma 54 mutant strain NZ7306 with and without peroxide treatment: A Lactobacillus plantarum strain with a deletion in the alternative sigma factor 54 (?54) encoding gene rpoN, displayed a 100 fold higher sensitivity to peroxide as compared to its parental strain. This feature could be due to ?54-dependent regulation of genes involved in peroxide stress response. However, transcriptome analyses of the wild type and the mutant strain during peroxide exposure did not support such a role for ?54. Subsequent experiments revealed that the impaired expression of the mannose PTS operon in the rpoN mutant caused the observed increased peroxide sensitivity. Keywords: genetic modification Two conditions were tested in the transcriptome comparison, the condition “peroxide stress exposure” and the condition “deletion of the rpoN-gene”. This resulted in 4 samples: “Wild type normal”, “rpoN-mutant normal”, “Wild type with peroxide”, and “rpoN-mutant with peroxide”. Samples were hybridised against a sample with only one variation, resulting in a total of 4 hybridisations (“Wild type vs Mutant”, “Wild type vs Wild type peroxide”, “Mutant vs Mutant peroxide”, and “Wild type peroxide vs Mutant peroxide”). The experiment was performed in duplicate (duplicates are designated A and B) and in order to discriminate the variation between the duplicates additional hybridisation were performed: “Wild type A vs Wild type B” and “Mutant with peroxide A vs Mutant with peroxide B”. This resulted in a total of 10 hybridisations (2 x 4 and 2).
2008-05-08 | E-GEOD-11351 | biostudies-arrayexpress
Project description:The goal of this study is to characterize a gshF::cam L. plantarum strain NZ7608. From phenotype characterization we have observed that the gene gshF plays a role in hydrogen peroxide resistance in L. plantarum and therefore we wanted to analyze the global transcriptome response of strain NZ7608 towards peroxide and compared this to wild type response. In this experiment we compared two L. plantarum strains: WCFS1 (wild type) and NZ7618 (gshF::cam). Both strains were grown -in duplo- on CDM containing 0.5% glucose at 37 degrees celsius. When cell density reached OD600=1.0 a hydrogen peroxide stress was given to the cultures to a final concentration of 10mM. Samples were taken at times (0 10 and 30 minutes) upon hydrogen peroxide. All withdrawn samples were used for this microarray experiment. Keywords: peroxide, gshF mutant
2008-01-09 | GSE9961 | GEO
Project description:To determine the genes in addition to fimA regulated by sigma 54 by analysing the gene expression profiles of an rpoN mutant compared to the D. nodosus wild-type strain. Keywords: genetic modification
2006-04-18 | GSE3465 | GEO
Project description:In this experiment we analyzed the impact of the disruption of trxB1in Lactobacillus plantarum at the transcriptome level. Furthermore we studied the effect of 3.5 mM peroxide effect on both Lactobacillus plantarum wild type (strain WCFS1) and a trxB1 mutant (strain NZ7608). Keywords: mutant analysis of trxB1, hydrogen peroxide stress
2007-08-09 | GSE8672 | GEO
Project description:The phytopathogen Xylella fastidiosa produces two classes of pili, long type IV pili and short type I pili, which are involved in motility and adhesion. In this work, we have investigated the role of Ï54 factor and its involvement in the regulation of fimbrial biogenesis in X. fastidiosa. An rpoN null mutant was constructed from citrus strain J1a12, and analyses of global gene expression profile by microarrays comparing the wild type and rpoN mutant strains showed that few genes exhibited differential expression. At least one gene, pilA1 (XF2542), which encodes the structural pilin protein of type IV fimbriae, showed decreased expression in the rpoN mutant whereas an operon encoding proteins of type I fimbriae were twofold more expressed in the mutant. Quantitative real time RT-PCR (qRT-PCR) analysis confirmed that pilA1 transcript was significantly reduced in the rpoN mutant. The transcriptional start site of pilA1 was determined by primer extension, and a canonical Ï54-dependent promoter was found upstream of the start site. Genome sequence analysis of X. fastidiosa revealed five paralogues of pilA, but microarray and qRT-PCR data demonstrated that only the pilA1 transcript was significantly affected in the rpoN mutant. The rpoN mutant made more biofilm than the wild type strain and presented a cell-cell aggregative phenotype. These results indicate that Ï54 regulates biofilm formation, probably via differential regulation of genes involved in type IV and type I fimbrial biogenesis. Direct comparison between wild type strain J1a12 and mutant strain rpoN-.
2010-06-25 | E-GEOD-8097 | biostudies-arrayexpress
Project description:The ability of C. albicans TLO genes to mediate oxidative stress responses was characterised by expressing CaTLO1 and CaTLO4 in a C. dubliniensis TLO null mutant. Each complemented strain was grown with and without peroxide. The transcript profile of peroxide vs no peroxide cultures was analysed in 4 biological replicates for both CaTLO1 and CaTLO4.
2018-02-13 | GSE110463 | GEO
Project description:In this experiment two strains were compared. The control strain was the wild type strain containing the plasmid, pCD341. pCD341 is an inducible expression vector, a plasmid which can be used to make a bacterium produce a protein of interest. It is called inducible, because the protein of interest will only be produced if an inducer, in this case, IPTG, is present. In the control strain pCD341 is "empty", meaning the gene encoding the protein of interest has not been inserted into the vector, so when you add IPTG nothing will be produced. Because producing plasmid and being exposed to IPTG can stress cells, the wild type strain harboring the "empty" plasmid was used as the control. The experimental strain DL1/pCD341RpoN contained the a "full" vector into which the gene for the sigma factor RpoN was been inserted. Thus when IPTG is added to the growth medium, this strain will overproduce RpoN. RpoN is an alternative sigma factor, a subunit of the RNA polymerase which is required for binding of the polymerase to specific promoters and is therefore required for the transcription of genes with these promoter sequences. Most bacteria have multiple sigma factors, many of which have specialized functions. In many other bacteria, RpoN is required for the expression of genes involved in nitrogen fixation. However, in G.sulfurreducens and myxococcus xanthus, RpoN appears to essential for survival under all conditions tested and its function and promoter specificity are not known. This experiment was performed in order to gain insight into the physiological function of G. sulfurreducens RpoN. Since we could not knock out RpoN, we decided to try overproducing it, hoping that overproducing RpoN would increase expression of genes who's promoters are recognized by RpoN. We took the wild type strain + empty vector and and the wild type strain with the RpoN vector and transferred them both into medium containing IPTG. For this experiment, we used batch cultures, or closed culture containers (no media nutrients or cells flowing in and out). We harvested cells at mid log phase for RNA preparation. There were three biological replicates and two replicate hybridizations were carried out for each. Keywords: cell type comparison
2009-07-13 | GSE8022 | GEO
Project description:RpoN (σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include alpha- and beta-rhizobia. Our previous studies showed that a rpoN mutant of the beta-rhizobial strain Paraburkholderia phymatum formed root nodules on Phaseolus vulgaris that were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by the P. phymatum rpoN Fix- mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix+ and Fix- nodules – combined with a search for RpoN binding sequences in promoter regions of regulated genes – confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also identified additional target genes, whose differential expression was able to explain the observed metabolite changes in a numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype by forming less but heavier nodules on P. vulgaris roots.
2018-06-06 | GSE111993 | GEO
Project description:The RpoN-RpoS alternative sigma factor pathway is essential for key adaptive responses by Borrelia burgdorferi, particularly those involved in the infection of a mammalian host. A putative response regulator, Rrp2, ostensibly is required for activation of the RpoN-dependent transcription of rpoS. However, questions remain regarding the extent to which the three major constituents of this pathway (Rrp2, RpoN, and RpoS) act interdependently. To assess the functional interplay between Rrp2, RpoN, and RpoS, we employed microarray analyses to compare gene expression levels in rrp2, rpoN, or rpoS mutants of parental strain 297. We identified 98 genes that were similarly regulated by Rrp2, RpoN and RpoS, and an additional 47 genes were determined to be likely regulated by this pathway. The substantial overlap between genes regulated by RpoS and RpoN provides compelling evidence that these two alternative sigma factors form a congruous pathway and that RpoN regulates B. burgdorferi gene expression through RpoS. Although several known B. burgdorferi virulence determinants were regulated by the RpoN-RpoS pathway, a defined function has yet to be ascribed to most of the genes substantially regulated by Rrp2, RpoN and RpoS, therefore providing additional avenues for future research into the genetic determinants contributing to virulence expression by B. burgdorferi. Keywords: gene profiling 297 (wt) vs rpoS mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates 297 (wt) vs rpoN mutant: 5 slides, 10 hybridizations (including dyeswaps), three biological replicates 297 (wt) vs rrp2 mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates 5A18 (wt) vs XY424.3 (rrp2 mutant): 5 slides, 10 hybridizations (including dyeswaps), three biological replicates 297 (wt) vs rpoS mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates 297 (wt) vs rpoN mutant: 5 slides, 10 hybridizations (including dyeswaps), three biological replicates 297 (wt) vs rrp2 mutant: 6 slides, 12 hybridizations (including dyeswaps), three biological replicates 5A18 (wt) vs XY424.3 (rrp2 mutant): 5 slides, 10 hybridizations (including dyeswaps), three biological replicates
2008-09-09 | E-GEOD-11284 | biostudies-arrayexpress
Project description:Fission yeast CSL mutants (cbf11 and cbf12 knock-outs) show altered sensitivity to hydrogen peroxide. To help elucidate the molecular basis of this phenomenon, we analyzed wild-type and mutant transcriptomes before stress and as a timecourse after treatment with hydrogen peroxide. Cells were grown to exponential phase in YES medium, untreated samples were collected (time 0), cells were treated with 0.74 mM hydrogen peroxide and harvested after 15 and 60 min post treatment. Total RNA was isolated, labelled and hybridized to custom-made two-colour microarrays. Each sample was hybridized against reference created by pooling equal aliquots from all 9 samples.
2021-11-03 | E-MTAB-6761 | biostudies-arrayexpress