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Global transcriptional response of Clostridium difficile carrying the ϕCD38-2 prophage

ABSTRACT: We used RNA-seq to conduct a genome-wide transcriptomic analysis of the C. difficile strain R20291 carrying the newly introduced ϕCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and PTS subunits involved in glucose, fructose and glucitol/sorbitol uptake and metabolism. Also of note, the presence of ϕCD38-2 upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was the conserved phase-variable cell wall protein CwpV, which was upregulated by about 20-fold in the lysogen. This is the first study describing the global response of C. difficile to the presence of a newly introduced prophage.

ORGANISM(S): Clostridioides difficile

PROVIDER: GSE56818 | GEO | 2014/12/22

SECONDARY ACCESSION(S): PRJNA244679

REPOSITORIES: GEO

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Global transcriptional response of Clostridium difficile carrying the M-OM-^UCD38-2 prophage

Project description:We used RNA-seq to conduct a genome-wide transcriptomic analysis of the C. difficile strain R20291 carrying the newly introduced M-OM-^UCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and PTS subunits involved in glucose, fructose and glucitol/sorbitol uptake and metabolism. Also of note, the presence of M-OM-^UCD38-2 upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was the conserved phase-variable cell wall protein CwpV, which was upregulated by about 20-fold in the lysogen. This is the first study describing the global response of C. difficile to the presence of a newly introduced prophage. Two strains (WT and lysogen) were subjected for RNA-seq analysis with two biological replicates each.

2014-12-22 | E-GEOD-56818 | biostudies-arrayexpress

Comparative genomic hybridization of Clostridium difficile strains to identify markers of different ribotypes

Project description:Clostridium difficile (C. difficile) strains belonging to PCR ribotype 027, PFGE type NAP1, REA type B1 and toxinotype III, termed NAP1/027, have been implicated in the increased frequency of outbreaks of Clostridium difficile-associated diarrhoea (CDAD) in North America and Europe. The NAP1/027 strains appears to be more virulent with an increased mortality and frequency of relapse. Current European C. difficile microarrays are designed to the first sequenced and annotated C. difficile complete genome - strain 630 (ribotype 12). A high density oligonucleotide microarray was designed to C. difficile 630 (CD630) sequence and extra probes corresponding to two PCR ribotypes O27 strains C. difficile R20291 and QCD-32g58 were also included. Comparative genomic hybridisation was used to identify markers of ribotype 027 strains and markers to identify CD630. Strains hybridised to the array included the most prevalent ribotypes found in the UK and Europe (106 and 001) as well as the emerging hypervirulent ribotype 078.

2010-07-01 | E-MTAB-162 | biostudies-arrayexpress

Clostridium difficile transcriptome of strain R20291 in response to cysteine by using a time-resolved RNA-seqencing

Project description:The incidence of Clostridium difficile infection has been steadily rising over the past decade. Its increased rate is associated with the specific NAP1/BI/027 strains which are “hypervirulent” and have led to several large outbreaks since their emergence. However, the relation between their outbreaks and virulence regulation mechanisms remains unclear. It has been reported that the major virulence factor TcdA and TcdB in C. difficile could be repressed by cysteine. Here, we investigated functional and virulence-associated regulation of C. difficile R20291 in response to cysteine stress by using a time-resolved genome-wide transcriptional analysis. Dramatic changes of gene expression in C. difficile were revealed in functional categories related to transport, metabolism, and regulators under cysteine stress during different phases of growth.

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Project description:Clostridium difficile epidemic strain R20291 was grown in presence of the two main bile acids, Deoxycholate and Cholate.

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Clostridioides difficile: R20291_pMTL84151 transconjugant (C) vs. R20291_pMTL84151-03890 (T1)

Project description:Gene expression level of Clostridioides difficile (C. difficile) strain R20291 comparing control C. difficile carring pMTL84151 as vector plasmid with C. difficile conjugated with a pMTL84151-03890 gene. Goal was to determine the effects of 03890 gene conjugation on C. difficile strain R20291 gene expression.

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Comparison of the expression profiles of R20291 strain and a R20291 strain after 4h, 6h, 8h, 14h, 38h of growth in vivo

Project description:Transcriptionnal profiling of C. difficile R20291 strain vs a R20291 strain after4h 6h 8h 14h 38h of growth in Vivo

2016-01-31 | GSE35726 | GEO

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Project description:Transcriptional analysis of Clostridium difficile R20291 in biofilm formation, planktonic state and grown on blood agar RNA sequencing was performed on Clostridium difficile R20291 in three different conditions: Biofilm formation, plantonic state and grown on blood agar plates. Each condtion has 3 replicates.

2016-05-18 | E-GEOD-69001 | biostudies-arrayexpress

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Project description:Clostridioides difficile BI/NAP1/ribotype 027 is an epidemic hypervirulent strain found worldwide, including in Latin America. We examined the genomes and exoproteomes of two multilocus sequence type (MLST) clade 2 C. difficile strains considered hypervirulent: ICC-45 (ribotype SLO231/UK[CE]821), isolated in Brazil, and NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica. C. difficile isolates were cultured and extracellular proteins were analyzed using high-performance liquid chromatography-tandem mass spectrometry. Genomic analysis revealed that these isolates shared most of the gene composition. Only 83 and 290 NAP1/027 genes were considered singletons in ICC-45 and NAP1/027, respectively. Exoproteome analysis revealed 197 proteins, of which 192 were similar in both strains. Only five proteins were exclusive to the ICC-45 strain. These proteins were involved with catalytic and binding functions and indirectly interacted with proteins related to pathogenicity. Most proteins, including TcdA, TcdB, flagellin subunit, and cell surface protein, were overrepresented in the ICC-45 strain; 14 proteins, including mature S-layer protein, were present in higher proportions in LIBA5756. These data show close similarity between the genome and proteins in the supernatant of two strains with hypervirulent features isolated in Latin America and underscore the importance of epidemiological surveillance of the transmission and emergence of new strains.

2021-07-01 | PXD026218 | Pride

Comparison of the expression profiles of R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in vivo

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