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| Status |
Public on Feb 28, 2011 |
| Title |
Regulon prediction of the sporulation factors Spo0A, SigF, SigE, and SigG in Clostridium acetobutylicum ATCC 824 |
| Organism |
Clostridium acetobutylicum ATCC 824 |
| Experiment type |
Expression profiling by array
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| Summary |
Clostridium acetobutylicum, the endospore-forming anaerobe best known for its ABE (acetone-butanol-ethanol) fermentation, has received renewed attention recently for the biological production of butanol, both for bulk chemical production and as a potential biofuel. With butanol production in mind, most of the recent research on C. acetobutylicum has focused on increasing butanol production, tolerance to butanol, and optimizing it for various substrates. However, an equally important trait, though less understood, is its sporulation program, which it coupled to solvent formation. The model organism for endospore formation is Bacillus subtilis, but significant physiological, metabolic, and genomic differences exist between the two organisms. Despite these differences, the major sporulation-related transcription/sigma factors are conserved between the two species. These transcription/sigma factors are activated in a cascade manner such that Spo0A becomes active first, followed by σF, then σE, then σG, and finally σK. The goal of this study is to determine the regulons of 4 of these transcription/sigma factors (Spo0A, σF, σE, and σG) and compare them to those in B. subtilis. To accomplish this goal, individual mutant strains were created for Spo0A, σF, σE, and σG, in which the transcription/sigma factor is silenced. These mutants were then compared transcriptionally using microarrays to determine the regulon of each transcription/sigma factor. To help avoid false positives, comparisons were made between strains in which the downstream transcription/sigma factor is silenced (e.g., for the Spo0A regulon, the Spo0A mutant was compared against the σF mutant and the σE mutant, since they are both upregulated by Spo0A) rather than just the WT. For each regulon, 4 timepoints were taken, since it is very difficult to synchronize sporulation in C. acetobutylicum cultures, and dye-swaps were prepared for each timepoint.
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| Overall design |
Four transcription/sigma factor regulons were investigated: Spo0A, σF, σE, and σG. For Spo0A, two comparison were made: Spo0A mutant vs σF mutant and Spo0A mutant vs σE mutant. For σF, two comparison were also made: σF mutant vs σE mutant and σF mutant vs σG mutant. Finally for σE and σG, only one comparison for each was made: σE mutant vs σG mutant and σG mutant vs wild-type, respectively. For each comparison, 4 timepoints were analyzed, and dye-swaps were prepared for each timepoint comparison. Timepoints were chosen based on when each transcription/sigma factor was expected to be active, based on a previous study [Jones, SW, et al. Genome Biol. 2008;9(7):R114.].
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| Contributor(s) |
Jones SW, Tracy BP, Chen Y, Papoutsakis ET |
| Citation(s) |
24187083 |
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| Submission date |
Sep 13, 2010 |
| Last update date |
Feb 06, 2014 |
| Contact name |
Eleftherios Terry Papoutsakis |
| E-mail(s) |
[email protected]
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| Organization name |
University of Delaware
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| Department |
Chemical Engineering
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| Street address |
15 Innovation Way
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
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| Platforms (1) |
| GPL10908 |
Clostridium acetobutylicum ATCC 824 transcriptional 44k v4 |
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| Samples (24)
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| GSM593191 |
Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 14) |
| GSM593192 |
Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 16) |
| GSM593193 |
Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 20) |
| GSM593194 |
Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 22) |
| GSM593195 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 14) |
| GSM593196 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 16) |
| GSM593197 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 20) |
| GSM593198 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 22) |
| GSM593199 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 22) |
| GSM593200 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 24) |
| GSM593201 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 26) |
| GSM593202 |
Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 28) |
| GSM593203 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 22) |
| GSM593204 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 24) |
| GSM593205 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 26) |
| GSM593206 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 28) |
| GSM593207 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 24) |
| GSM593208 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 26) |
| GSM593209 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 30) |
| GSM593210 |
Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 32) |
| GSM593211 |
Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 28) |
| GSM593212 |
Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 30) |
| GSM593213 |
Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 34) |
| GSM593214 |
Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 36) |
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| Relations |
| BioProject |
PRJNA130309 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE24103_RAW.tar |
580.6 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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