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| Status |
Public on Aug 10, 2013 |
| Title |
Global analysis of genes induced during sporulation of Clostridium difficile |
| Organism |
Clostridioides difficile 630 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Fimlaid KA, Shen A |
| Citation(s) |
23950727 |
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| Submission date |
Apr 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Aimee Shen |
| E-mail(s) |
[email protected]
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| Organization name |
University of Vermont
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| Department |
Microbiology and Molecular Genetics
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| Lab |
Shen Lab
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| Street address |
Stafford Hall rm 308, 95 Carrigan Drive
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| City |
Burlington |
| State/province |
Vermont |
| ZIP/Postal code |
05405 |
| Country |
USA |
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| Platforms (1) |
| GPL18533 |
Illumina HiSeq 1000 (Peptoclostridium difficile 630) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA196825 |
| SRA |
SRP020944 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45977_ProcessedDataColumns_README.txt |
18.4 Kb |
(ftp)(http) |
TXT |
| GSE45977_RAW.tar |
850.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE45977_sigMuts_Final_20130620.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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