D. nodosus WT vs pilR mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Dichelobacter nodosus
PROVIDER: GSE3466 | GEO | 2006/04/18
SECONDARY ACCESSION(S): PRJNA93409
REPOSITORIES: GEO
Similar Datasets
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:Transcriptional profiling of K. pneumoniae comparing the wild type strain (S5) with a hfq deletion mutant (H0201). Goal was to determine the effects of Hfq absence on global K. pneumoniae gene expression.
2013-01-11 | GSE29448 | GEO
Project description:E. coli K-12 BW25113 mutant strain hha expression in biofilm cells relative to E. coli wild-type strain expression in biofilm cells. Samples were cultured in LB with glasswool at 37C for 4 hours and in LB glu with glasswool at 37C for 4, 15 and 24 hours. Hha is a temperature- and osmolarity-dependent modulator of gene expression that is induced 30-fold in Escherichia coli biofilms. Here we show through whole-transcriptome analysis that Hha decreases biofilm formation in both LB and LB glu media by (i) repressing fliC encoding the main structural flagellar protein flagellin, (ii) by repressing fimA encoding the major structural subunit of type I fimbriae, (iii) by repressing ihfA encoding a subunit of the transcriptional regulator IHF that induces the transcription of type I fimbriae genes, (iv) by regulating tnaA encoding tryptophanase that inhibits biofilms, and (v) by repressing ybaJ that forms an operon with hha. Corroborating the microarray data, hha deletion increased motility 3.2 ± 0.1-fold, decreased extracellular indole concentrations 12 ± 2-fold, and decreased type I fimbriae (as measured by yeast agglutination). Biofilm tests using single and double mutants of fimA and ihfA and transcriptional studies of the fimA, ihfA and ybaJ-hha promoters confirmed that Hha represses biofilm by inhibiting type I fimbriae production and that it negatively regulates its own transcription and that of ybaJ. Nickel-enhanced DNA microarrays to determine in vivo Hha binding sites confirmed that Hha binds the ybaJ-hha promoter, that it binds fimZ, a positive regulator of fimA, and that it binds to the rare codon tRNAs argU, ileXY, and proL. Sequence analysis of fimZ, fimB, fimE, and the type I fimbriae gene cluster fimAICDFGH revealed a high bias for the rare codons of arginine, isoleucine, proline, leucine, and threonine, and overexpressing Hha leads to cell death. Therefore, it appears Hha decreases biofilms by decreasing type I fimbriae production as a result of inhibiting synthesis of tRNAs for rare codons. Keywords: effect of hha deletion in biofilm formation 4 hr LB and 4,15 and 24 hr LB glu
2008-06-17 | GSE8708 | GEO
Project description:Salmonella enterica serotype Typhimurium produces a variety of fimbrial appendages, among which the type 1 fimbriae is the most common type. In vitro static broth culture favors S. Typhimurium to produce type 1 fimbriae, while solid agar inhibits its expression. A transposon inserted in the stbC gene, which would encode an usher protein for Stb fimbriae of a non-flagellar S. Typhimurium LB5010 strain, conferred it to agglutinate yeast cells on both cultures, and was mannose-sensitive. Reverse transcription polymerase chain reaction (RT-PCR) revealed that the expression of the fimbrial major subunit gene fimA, and fimZ, a positive regulator gene of fimA, were both increased in the stbC mutant strain when grown on LB agar; fimW, a repressor gene of fimA, exhibited lower expression. Flagella were observed in the stbC mutant and this phenotype was correlated with the motile phenotype detected by MSRV agar medium and reaction with flagella antiserum. Microarray data and RT-PCR also indicated that the expression of three genes, motA, motB, and cheM, was enhanced in the stbC mutant. The S. Typhimurium stbC mutant was resistant to a variety of antibiotics, consistent with the finding that expression of yhcQ and ramA, two genes involved in multidrug resistance, was enhanced. A complementation test revealed that transforming a recombinant plasmid possessing the coding sequence of the stbC gene restored the mannose-sensitive agglutination phenotype to the stbC mutant much as that in the parental S. Typhimurium LB5010 strain, indicating the possibility of an interplay of different fimbrial systems in coordinating their expression. Key Words: Salmonella enterica serotype Typhimurium, fimbriae, type 1 fimbriae, stbC, transposon, multidrug resistant, flagella
2011-12-25 | GSE34685 | GEO
Project description:Transcriptional profiling of Bmi1 mutant dental epithelia including the stem cell compartment to determine which genes are upregulated in response to loss of Bmi1.
2013-04-12 | GSE45999 | GEO
Project description:Salmonella enterica serotype Typhimurium produces a variety of fimbrial appendages, among which the type 1 fimbriae is the most common type. In vitro static broth culture favors S. Typhimurium to produce type 1 fimbriae, while solid agar inhibits its expression. A transposon inserted in the stbC gene, which would encode an usher protein for Stb fimbriae of a non-flagellar S. Typhimurium LB5010 strain, conferred it to agglutinate yeast cells on both cultures, and was mannose-sensitive. Reverse transcription polymerase chain reaction (RT-PCR) revealed that the expression of the fimbrial major subunit gene fimA, and fimZ, a positive regulator gene of fimA, were both increased in the stbC mutant strain when grown on LB agar; fimW, a repressor gene of fimA, exhibited lower expression. Flagella were observed in the stbC mutant and this phenotype was correlated with the motile phenotype detected by MSRV agar medium and reaction with flagella antiserum. Microarray data and RT-PCR also indicated that the expression of three genes, motA, motB, and cheM, was enhanced in the stbC mutant. The S. Typhimurium stbC mutant was resistant to a variety of antibiotics, consistent with the finding that expression of yhcQ and ramA, two genes involved in multidrug resistance, was enhanced. A complementation test revealed that transforming a recombinant plasmid possessing the coding sequence of the stbC gene restored the mannose-sensitive agglutination phenotype to the stbC mutant much as that in the parental S. Typhimurium LB5010 strain, indicating the possibility of an interplay of different fimbrial systems in coordinating their expression. Key Words: Salmonella enterica serotype Typhimurium, fimbriae, type 1 fimbriae, stbC, transposon, multidrug resistant, flagella RNA transcript of Salmonella Typhimurium LB5010 strain comparing wild-type with stbC mutant. Two-cindition experiment, wild-type vs. stbC mutant strain.
2011-12-25 | E-GEOD-34685 | biostudies-arrayexpress
Project description:Background: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that must successfully adapt to the broad fluctuations in the concentration of dissolved dioxygen encountered in the host. In Escherichia coli, ArcA (Aerobic Respiratory Control) helps the cells to sense and respond to the presence of dioxygen. The global role of ArcA in E. coli is well characterized; however, little is known about its role in anaerobically grown S. Typhimurium. Results: We compared the transcriptional profiles of the virulent wild-type (WT) strain (ATCC 14028s) and its isogenic arcA mutant grown under anaerobic conditions. We found that ArcA directly or indirectly regulates 392 genes (8.5% of the genome); of these, 138 genes are poorly characterized. Regulation by ArcA in S. Typhimurium is similar, but distinct from that in E. coli. Thus, genes/operons involved in core metabolic pathways (e.g., succinyl-CoA, fatty acid degradation, cytochrome oxidase complexes, flagellar biosynthesis, motility, and chemotaxis) were regulated similarly in the two organisms. However, genes/operons present in both organisms, but regulated differently by ArcA in S. Typhimurium included those coding for ethanolamine utilization, lactate transport and metabolism, and succinate dehydrogenases. Salmonella-specific genes/operons regulated by ArcA included those required for propanediol utilization, flagellar genes (mcpAC, cheV), Gifsy-1 prophage genes, and a few SPI-3 genes (mgtBC, slsA, STM3784). In agreement with our microarray data, the arcA mutant was non-motile, lacked flagella, and was as virulent in mice as the WT. Furthermore, we identified a set of 120 genes whose regulation was shared with the anaerobic redox regulator, Fnr. Conclusion(s): We have identified the ArcA regulon in anaerobically grown S. Typhimurium. Our results demonstrated that in S. Typhimurium, ArcA serves as a transcriptional regulator coordinating cellular metabolism, flagella biosynthesis, and motility. Furthermore, ArcA and Fnr share in the regulation of 120 S. Typhimurium genes.
2011-02-10 | GSE24564 | GEO
Project description:Transcriptional profiling of K. pneumoniae comparing the wild type strain (S5) with a hfq deletion mutant (H0201). Goal was to determine the effects of Hfq absence on global K. pneumoniae gene expression. WT vs. Hfq mutant. Eight replicates for each ORF presented in the 44K array.
2013-01-11 | E-GEOD-29448 | biostudies-arrayexpress
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
2008-05-08 | GSE11351 | GEO
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