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| Status |
Public on Nov 01, 2020 |
| Title |
Sulfate assimilation in Clostridium thermocellum |
| Organism |
Acetivibrio thermocellus DSM 1313 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Investigation of sulfur metabolism in Clostridium thermocellum DSM 1313 ∆hpt, to determine growth and gene expression when the organism is incubated with either the oxidized (i.e., sulfate) or the reduced and assimilated (i.e., cysteine) forms of sulfur. A sulfite reductase (∆hpt ∆SO3R) knockout mutant to limit sulfur assimilation was created to compare the resulting gene expression patterns by RNAseq transciptomics against the parental strain (∆hpt) when both are grown in the presence of sulfate. Additionally, we bypass the sulfate auxotrophy of the mutant by providing assimilated sulfur in the form of cysteine to determine whether growth is restored to normal and whether methionine can be biosynthesized by yet uncharacterized pathways in this organism.
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| Overall design |
Samples for RNA-seq were taken from mid-exponential phase (OD ~ 0.6) batch cultures grown in MTC on 5 g/l cellobiose. Control strain (∆hpt) and sulfite-reductase-mutant strain (∆hpt∆SO3R) were grown in the presence of either 5.7mM cysteine or 28.2mM sodium sulfate as the only sulfur source
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| Contributor(s) |
Dumitrache A, Brown SD, Rodriquez M Jr, Klingeman DM |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jun 14, 2017 |
| Last update date |
Nov 01, 2020 |
| Contact name |
Dawn Marie Klingeman |
| E-mail(s) |
[email protected]
|
| Phone |
+18655763435
|
| Organization name |
Oak Ridge National Lab
|
| Department |
Biosciences Division
|
| Lab |
RNA Profiling
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| Street address |
1 Bethel Valley Rd building 15056 Rm 366 MS 6038
|
| City |
Oak Ridge |
| State/province |
TN |
| ZIP/Postal code |
37831-6342 |
| Country |
USA |
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| Platforms (1) |
| GPL20122 |
Illumina HiSeq 2500 (Ruminiclostridium thermocellum DSM 1313) |
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| Samples (12)
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| GSM2668671 |
PTR-1 (Clostridium thermocellum 1313 ∆hpt: cysteine) |
| GSM2668672 |
PTR-2 (Clostridium thermocellum 1313 ∆hpt: cysteine) |
| GSM2668673 |
PTR-3 (Clostridium thermocellum 1313 ∆hpt: cysteine) |
| GSM2668674 |
PSR-1 (Clostridium thermocellum 1313 ∆hpt: sulfate) |
| GSM2668675 |
PSR-2 (Clostridium thermocellum 1313 ∆hpt: sulfate) |
| GSM2668676 |
PSR-3 (Clostridium thermocellum 1313 ∆hpt: sulfate) |
| GSM2668677 |
MTR-1 (Clostridium thermocellum 1313 ∆hpt∆SO3R: cysteine) |
| GSM2668678 |
MTR-2 (Clostridium thermocellum 1313 ∆hpt∆SO3R: cysteine) |
| GSM2668679 |
MTR-3 (Clostridium thermocellum 1313 ∆hpt∆SO3R: cysteine) |
| GSM2668680 |
MSR-1 (Clostridium thermocellum 1313 ∆hpt∆SO3R: sulfate) |
| GSM2668681 |
MSR-2 (Clostridium thermocellum 1313 ∆hpt∆SO3R: sulfate) |
| GSM2668682 |
MSR-3 (Clostridium thermocellum 1313 ∆hpt∆SO3R: sulfate) |
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| Relations |
| BioProject |
PRJNA390549 |
| SRA |
SRP109227 |
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