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Series GSE31672 Query DataSets for GSE31672
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
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.
 
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.
 
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 wittink@science.uva.nl
Phone +31205257937
Fax -
URL http://www.micro-array.nl
Organization name Universiteit van Amsterdam
Department MAD
Lab MAD
Street address Kruislaan 318
City Amsterdam
State/province -
ZIP/Postal code 1098 SM
Country Netherlands
 
Platforms (1)
GPL6546 Agilent-016989 Synechocystis sp. PCC 6803 8x15K custom array
Samples (26)
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
Relations
BioProject PRJNA145379

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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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