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Series GSE69981 Query DataSets for GSE69981
Status Public on Sep 15, 2015
Title In vivo recruitment analysis and a mutant strain without any group 2 σ factors reveal roles of different σ factors in cyanobacteria
Organism Synechocystis sp. PCC 6803
Experiment type Expression profiling by array
Summary In eubacteria, replacement of one σ factor in the RNA polymerase (RNAP) holoenzyme by another one changes the transcription pattern. Cyanobacteria are eubacteria characterized by oxygenic photosynthesis and they typically encode numerous group 2 σ factors that closely resemble the essential primary σ factor. A mutant strain of the model cyanobacterium Synechocystis sp. PCC 6803 without functional group 2 σ factors (named as ΔsigBCDE) could not acclimate to heat, high salt, or bright light stress but in standard conditions ΔsigBCDE grew only 9% slower than the control strain. One-fifth of the genes in ΔsigBCDE were differently expressed compared to the control strain in standard growth conditions and several physiological changes in photosynthesis, and pigment and lipid compositions were detected. To directly analyze the σ factor content of RNAP holoenzyme in vivo, a His-tag was added to the γ subunit of RNAP in Synechocystis and RNAPs were collected. The results revealed that all group 2 σ factors were recruited by RNAP in standard conditions, but recruitment of SigB and SigC increased in heat stress, SigD in bright light, SigE in darkness and SigB, SigC and SigE in high salt, explaining the poor acclimation of ΔsigBCDE to these stress conditions.
Overall design Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and a mutant strain without any functional group 2 sigma factors, ΔsigBCDE, were harvested (A730=1, 40 mL) directly from standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2). From three to four independent experiments were performed at each conditions.
Contributor(s) Tyystjarvi T, Gunnelius L, Hakkila K, Matthijs HC
Citation(s) 26354085, 29985458
Submission date Jun 18, 2015
Last update date May 17, 2019
Contact name Taina Tyystjarvi
Organization name University of Turku
Department Biochemistry
Lab Molecular Plant Biology
Street address Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor
City Turku
ZIP/Postal code 20520
Country Finland
Platforms (1)
GPL17595 Agilent-016989 Synechocystis array [ORF version]
Samples (7)
GSM1715060 CS_standard_biol.rep1 [re-analysis]
GSM1715061 CS_standard_biol.rep2 [re-analysis]
GSM1715062 CS_standard_biol.rep3 [re-analysis]
BioProject PRJNA287323

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
GSE69981_RAW.tar 5.3 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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