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Title: Global analysis of genes induced during sporulation of Clostridium difficile      
dateReleased:
08-10-2013
description:
Purpose: The goal of this study was to identify genes whose expression is induced during sporulation in a Spo0A-, σF-, σE-, σG-, and σK-dependent manner. Methods: Whole genome RNA sequencing was performed on wildtype, spo0A-, sigF-, sigE-, sigG-, and sigK- C. difficile strains (strain 630 background; JIR8094 = parent strain), and the transcriptional profiles of the different mutants during growth on 70:30 agar plates were determined using an Illumina HiSeq1000. Results: This analysis identified 185 genes whose expression is collectively activated by sporulation sigma factors: 150 were σF-dependent, 150 were σE-dependent, 30 were σG-dependent, and 31 were σK-dependent. A total of 237 genes were identified as requiring Spo0A for their expression when sporulation was induced on the 70:30 plates. Conclusions: These results provide the first genome-wide transcriptional analysis of genes whose expression is induced by specific sporulation sigma factors in the Clostridia and highlight that diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes. For example, in contrast with the B. subtilis sporulation pathway, C. difficile σE was not required to fully activate σG, and σG was not required to activate σK. Wildtype, spo0A-, sigF-, sigE-, sigG-, and sigK- were streaked onto 70:30 plates in triplicate, and sporulation was induced. RNA from the three biological replicate samples was harvested, DNAse-I treated, and ribosomally depleted using Ribo-Zero kits. This RNA was transformed into cDNA, and the resulting libraries were subjected to paired end sequencing using an Illumina HiSeq 1000.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-45977
refinement:
raw
alternateIdentifiers:
45977
keywords:
functional genomics
dateModified:
05-03-2014
availability:
available
types:
gene expression
name:
Clostridium difficile 630
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-45977/E-GEOD-45977.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-45977/E-GEOD-45977.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45977
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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