Salmonella Newport allelic variation
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REPOSITORIES: ENA
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Project description:Salmonella enterica serovar Typhimurium produces type 1 fimbriae on the outer membrane and such hair-like appendages is proposed to play a significant role in the attachment of the bacteria to host cells and tissues. S. Typhimurium cultured in static broth favors expression of type 1 fimbriae. Conversely, solid agar medium represses type 1 fimbrial expression. Production of type 1 fimbriae is cooperatively regulated by fimZ, fimY, stm0551, fimW, and fimU within the fim gene cluster. FimZ belongs to the response regulator of the two-component regulatory system in bacteria and functions as a DNA binding protein. FimZ can bind to the promoter of the fimbrial major subunit gene fimA to activate its expression and produce type 1 fimbriae. A fimZ mutant in LB5010 strain constructed by allelic exchange was found to be non-fimbriate. Total RNA was extracted from the parental LB5010 and the fimZ mutant strain cultured in static broth and analyzed by hybridization to a S. Typhimurium LT2 DNA microarray. Transcriptomic analysis indicated that the stress response related gene cpxP, soxS and type 1 fimbriae related genes were down-regulated, whereas plasmid-encoded fimbriae, flagella associated genes and virulence genes like virK and mgtC were up-regulated in the fimZ mutant strain. It is possible that FimZ protein may play a role to interact with other genes besides fim genes. Mechanisms of this crosstalk warrant further elucidation.
2017-01-20 | GSE93882 | GEO
Project description:Fimbriae are hair-like structures present on the outer membrane of many Enterobacteriaceae and such appendages are proposed to play a significant role in the attachment of the bacteria to host cells and tissues. Salmonella enterica serovar Typhimurium has the potential to produce 13 different fimbrial types, among which type 1 fimbriae is the most common found. Expression of type 1 fimbriae is cooperatively controlled by fimZ, fimY, stm0551, fimW, and fimU within the fim gene cluster. FimZ belongs to the response regulator of the two-component regulatory system in bacteria and functions as a DNA binding protein. FimZ is a positive regulator for type 1 fimbrial expression in S. Typhimurium. A fimZ mutant in ATCC 14028 strain constructed by allelic exchange did not produce type 1 fimbriae. Total RNA was extracted from the parental ATCC 14028 and its fimZ mutant cultured in static broth and analyzed by hybridization to a S. Typhimurium LT2 DNA microarray. Transcriptomic analysis indicated that the type 1 fimbriae related genes, multidrug efflux protein gene acrF were down-regulated, whereas flagella associated genes, chemotaxis and virulence genes such as invF and invH genes were up-regulated in the fimZ mutant strain. It is possible that FimZ protein may play a role to interact with other genes besides regulating type 1 fimbriae.
2017-08-12 | GSE102575 | GEO
Project description:The 5' untranslated region (UTR) sequence of eukaryotic mRNAs may contain upstream open reading frames (uORFs), which can regulate translation of the main open reading frame (mORF). The current model of translational regulation by uORFs posits that when a ribosome scans an mRNA and encounters a uORF, translation of that uORF can prevent ribosomes from reaching the mORF and cause decreased mORF translation. In this study, we first observed that rare variants in the 5' UTR dysregulate protein abundance. Upon further investigation, we found that rare variants near the start codon of uORFs can repress or derepress mORF translation, causing allelic changes in protein abundance. This finding holds for common variants as well, and common variants that modify uORF start codons also contribute disproportionately to metabolic and whole-plant phenotypes, suggesting that translational regulation by uORFs serves an adaptive function. These results provide evidence for the mechanisms by which natural sequence variation modulates gene expression, and ultimately, phenotype.
2021-11-02 | PXD026378 | Pride
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: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:Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3,073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we constructed a massively parallel reporter assays (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into Epstein-Barr virus-transformed B cell line GM12878 revealed 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Combined with allelic enhancer activity analyses in Jurkat cell line, we identified shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around 51 allelic variants identified one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second, larger class of TFs that also bind allelically but do not have their motifs directly altered by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE.
2021-01-31 | GSE143792 | GEO
Project description:Genome-wide association studies (GWAS) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium (LD) makes it challenging to discern causal variants. Computational finemapping prioritized thousands of credible variants, ~98% of which lie within poorly characterized non-coding regions. To functionally validate their regulatory effects, we performed a massively parallel reporter assay (MPRA) on 5,173 finemapped schizophrenia GWAS variants in primary human neural progenitors (HNPs). We identified 440 variants with allelic regulatory effects (MPRA-positive variants), with 72% of GWAS loci containing at least one MPRA-positive variant. Transcription factor binding had modest predictive power for predicting the allelic activity of MPRA-positive variants, while GWAS association, finemap posterior probability, enhancer overlap, and evolutionary conservation failed to predict MPRA-positive variants. Furthermore, 64% of MPRA-positive variants did not exhibit eQTL signature, suggesting that MPRA could identify yet unexplored variants with regulatory potentials. MPRA-positive variants differed from eQTLs, as they were more frequently located in distal neuronal enhancers. Therefore, we leveraged neuronal 3D chromatin architecture to identify 273 genes that physically interact with MPRA-positive variants. These genes annotated by chromatin interactome displayed higher mutational constraints and regulatory complexity than genes annotated by eQTLs, recapitulating a recent finding that eQTL- and GWAS-detected variants map to genes with different properties. Finally, we propose a model in which allelic activity of multiple variants within a GWAS locus can be aggregated to predict gene expression by taking chromatin contact frequency and accessibility into account. In conclusion, we demonstrate that MPRA can effectively identify functional regulatory variants and delineate previously unknown regulatory principles of schizophrenia.
2023-08-07 | GSE211045 | GEO
Project description:The multidrug-resistant (MDR) Salmonella enterica serotype Newport strain that produces CMY-2 beta-lactamase (Newport MDR-AmpC) was the source of sporadic cases and outbreaks in humans in France during 2000-2005. Because this strain was not detected in food animals, it was most likely introduced into France through imported food products.
| S-EPMC2600296 | biostudies-literature
Project description:We have exploited a spontaneously isolated mutant IgaA(T191P) that is near-maximally activated for the Rcs system, to identify a vast set of genes that respond, and report new regulatory properties of this signaling system in Salmonella enterica serovar Typhimurium. Microarray data show that the Rcs system normally functions as a positive regulator of SPI-2 and other genes important for growth of Salmonella in macrophages, although when highly activated, the system completely represses the SPI-1/SPI-2 virulence, flagellar, and fimbrial biogenesis pathways. The auxilliary protein RcsA, which works with RcsB to positively regulate colanic acid and other target genes, not only stimulates but also antagonizes the positive regulation of many genes in the igaA mutant. We show that RcsB represses motility through the 'RcsB box' in the promoter region of the master operon flhDC, and that RcsA is not required for this regulation. Curiously, RcsB selectively stimulates expression of the flagellar Type 3 secretion genes fliPQR; an RcsAB box located downstream of fliR influences this regulation. We show that excess colanic acid impairs swimming and inhibits swarming motility, consistent with the inverse regulation of the two pathways by the Rcs system. The work was published in Journal of Bacteriology: Wang Q, Zhao Y, McClelland M, Harshey RM. The RcsCDB signaling system and swarming motility in Salmonella enterica serovar Typhimurium: dual regulation of flagellar and SPI-2 virulence genes. J Bacteriol. 2007 Sep 28; [Epub ahead of print] PMID: 17905992 [PubMed - as supplied by publisher] Keywords: Comparative genomic hybridization
2008-06-25 | GSE9584 | GEO