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Title: The global response regulator RegR controls expression of denitrification genes in Bradyrhizobium japonicum      
dateReleased:
09-01-2014
description:
Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544), or cy2 (bll2388), genes involved in nitric oxide detoxification (blr2806-09), copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130 which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5’end of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS. A total of eight Affymetrix GeneChips are included in this study. Per strain (wild-type B. japonicum 110spc4, delta regR mutant 2426) four biological replicates were processed and analyzed. Strains were grown under anoxic conditions in Bergersen minimal medium supplemented with succinate as carbon source and KNO3 as terminal electron acceptor. For comparison, a microarray expression dataset generated with B. japonicum wild-type (Hauser et al., Mol. Genet. Genomics 278:255-271, 2007) and delta regR mutant cells (Lindemann et al., J. Bacteriol. 189:8928-8943, 2007) was used.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-56668
refinement:
raw
alternateIdentifiers:
56668
keywords:
functional genomics
dateModified:
09-06-2014
availability:
available
types:
gene expression
name:
Bradyrhizobium japonicum
ID:
A-GEOD-3401
name:
Affymetrix custom Bradyrhizobium japonicum strain USDA 110 19K array
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-56668/E-GEOD-56668.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-56668/E-GEOD-56668.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=GSE56668
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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