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Title: In vivo recruitment analysis and a mutant strain without any group 2 σ factors reveal roles of different σ factors in cyanobacteria      
dateReleased:
09-15-2015
description:
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. 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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-69981
refinement:
raw
alternateIdentifiers:
69981
keywords:
functional genomics
dateModified:
09-20-2015
availability:
available
types:
gene expression
name:
Synechocystis sp. PCC 6803
ID:
A-GEOD-17595
name:
Agilent-016989 Synechocystis array [ORF version]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-69981/E-GEOD-69981.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-69981/E-GEOD-69981.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69981
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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