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| Status |
Public on Dec 30, 2011 |
| Title |
Comparison of carboxysomal (ccmM) and photorespiratory (glcD1/D2) mutants of Synechocystis sp. PCC 6803 using metabolic and transcriptomic phenotyping |
| Organism |
Synechocystis sp. PCC 6803 |
| Experiment type |
Expression profiling by array
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| Summary |
The general acclimation of cyanobacteria to low carbon (LC) conditions includes coordinated alterations of gene expression and metabolism. To analyze possible signals for LC sensing and compensating reactions, we compared wild-type (WT) cells with two mutants of Synechocystis, the carboxysome-less mutant ccmM and the photorespiratory mutant ΔglcD1/D2. Metabolic phenotyping revealed that the mutant ΔccmM accumulated high 2-phosphoglycolate (2PG) levels while the ΔglcD1/D2 mutant accumulated glycolate, indicating oxygenase activity of RubisCO at high carbon (HC). The changes in the metabolite spectrum were compared to alterations in the global gene expression pattern. Cells of HC-grown mutants ΔccmM and ΔglcD1/D2 showed altered mRNA levels for many genes involved in photosynthesis, high light stress, and N-assimilation, while LC-specific genes such as those for inorganic carbon (Ci) transporters were not increased. After a shift to LC, mutant ΔglcD1/D2 revealed gene expression changes similar to WT cells, while mutant ΔccmM showed no differential expression of most LC-induced genes under identical conditions. In fact, none of the genes for Ci transporters or other components of the carbon concentrating mechanism (CCM) displayed higher transcript levels in the ΔccmM mutant. This finding renders a direct role for 2PG as a metabolic signal component for the induction of CCM during LC acclimation less likely. Because, the transcription pattern of ΔglcD1/D2 under LC showed specific differences compared to WT, a potential role for glycolate as a signal molecule that may trigger expression of parts of the CCM is proposed.
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| Overall design |
Transcriptional profiling of carboxysomal and photorespiratory mutants of Synechocystis sp. PCC 6803 under high carbon (HC) and low carbon (LC) conditions relative to the wildtype response.
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| Contributor(s) |
Hackenberg C, Huege J, Engelhardt A, Wittink F, Laue M, Matthijs HC, Kopka J, Bauwe H, Hagemann M |
| Citation(s) |
22096149 |
| Submission date |
Aug 25, 2011 |
| Last update date |
Jul 14, 2014 |
| Contact name |
Floyd Wittink |
| E-mail(s) |
wittink@science.uva.nl
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| Phone |
+31205257937
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| Fax |
-
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| URL |
http://www.micro-array.nl
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| Organization name |
Universiteit van Amsterdam
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| Department |
MAD
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| Lab |
MAD
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| Street address |
Kruislaan 318
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| City |
Amsterdam |
| State/province |
- |
| ZIP/Postal code |
1098 SM |
| Country |
Netherlands |
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| Platforms (1) |
| GPL6546 |
Agilent-016989 Synechocystis sp. PCC 6803 8x15K custom array |
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| Samples (26)
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| GSM786211 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 1_4a |
| GSM786212 |
Wildtype Synechocystis sp. PCC 6803 under 24h low carbon, replica 1_4 |
| GSM786213 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 2_4a |
| GSM786214 |
Wildtype Synechocystis sp. PCC 6803 under 24h low carbon, replica 2_4 |
| GSM786215 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 1_2 |
| GSM786216 |
Synechocystis mutant ccmM (sll1031) under 24h high carbon, replica 1_2 |
| GSM786217 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 2_2 |
| GSM786218 |
Synechocystis mutant ccmM (sll1031) under 24h high carbon, replica 2_2 |
| GSM786219 |
Synechocystis mutant ccmM (sll1031) under low carbon, replica 1_3 |
| GSM786220 |
Synechocystis mutant ccmM (sll1031) under 24h high carbon, replica 1_3 |
| GSM786221 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 24h low carbon, replica 1_4 |
| GSM786222 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 24h high carbon, replica 1_4 |
| GSM786223 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 24h low carbon, replica 2_4 |
| GSM786224 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 24h high carbon, replica 2_4 |
| GSM786225 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 1_4b |
| GSM786226 |
Wildtype Synechocystis sp. PCC 6803 under 3h low carbon, replica 1_4 |
| GSM786227 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 2_4b |
| GSM786228 |
Wildtype Synechocystis sp. PCC 6803 under 3h low carbon, replica 2_4 |
| GSM786229 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 1_3 |
| GSM786230 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under high carbon, replica 1_3 |
| GSM786231 |
Wildtype Synechocystis sp. PCC 6803 under 24h high carbon, replica 2_3 |
| GSM786232 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 24h high carbon, replica 2_3 |
| GSM786233 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 3h low carbon, replica 1_2 |
| GSM786234 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 24h high carbon, replica 1_2 |
| GSM786235 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 3h low carbon, replica 2_2 |
| GSM786236 |
Synechocystis double-mutant ∆glcD1/∆glcD2 under 24h high carbon, replica 2_2 |
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| Relations |
| BioProject |
PRJNA145379 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31672_RAW.tar |
105.2 Mb |
(http)(custom) |
TAR (of TXT) |
| Raw data provided as supplementary file |
| Processed data included within Sample table |
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