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Series GSE51647 Query DataSets for GSE51647
Status Public on Jan 30, 2014
Title The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria
Organism Synechocystis sp. PCC 6803
Experiment type Expression profiling by array
Summary The catalytic core of the RNA polymerase of most eubacteria is composed of two α subunits and β, β’ and ω subunits. In Escherichia coli, the ω subunit (encoded by the rpoZ gene) has been suggested to assist β’ during RNA polymerase core assembly. The function of the ω subunit is particularly interesting in cyanobacteria because the cyanobacterial β’ is split to N-terminal γ and C-terminal β’ subunits. The ∆rpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions although the mutant cells showed low light-saturated photosynthetic activity, low Rubisco content and accumulated high quantities of protective carotenoids and α-tocopherol. The ∆rpoZ strain contained 15% less of the primary σ factor, SigA, than the control strain, and recruitment of SigA to the RNA polymerase core was inefficient in ∆rpoZ. Thus, a cyanobacterial RNA polymerase holoenzyme lacking the ω subunit contains less frequently the primary σ factor. A DNA microarray analysis revealed that this leads to specific down-regulation of highly expressed genes, like genes encoding subunits for Rubisco, ATP synthase, NADH-dehydrogenase and carbon concentrating mechanisms. On the contrary, many genes showing only low or moderate expression in the control strain were up-regulated in ∆rpoZ. A conserved -10 region was detected in promoters showing up or down-regulation in ∆rpoZ, but -35 regions of down-regulated genes completely differed from -35 regions of up-regulated genes.
Overall design Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and RNA polymerase omega subunit inactivation strain, ΔrpoZ, 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) 24476911
Submission date Oct 24, 2013
Last update date Oct 16, 2015
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)
GSM1250061 CS_standard_biol.rep1 (reanalysis)
GSM1250062 CS_standard_biol.rep2 (reanalysis)
GSM1250063 CS_standard_biol.rep3 (reanalysis)
BioProject PRJNA224191

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
GSE51647_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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