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Title: Antagonistic regulation of motility and other cellular functions by RpoN and RpoS in Escherichia coli      
dateReleased:
12-04-2010
description:
Bacteria generally possess multiple σ factors that, based on structural and functional similarity, divide into two families: σD and σN. Among the seven σ factors in Escherichia coli, six belongs to the σD family. Each σ factor recognizes a group of promoters, providing effective control of differential gene expression. Many studies have shown that σ factors of the σD family compete with each other for function. In contrast, the competition between σN and σD families has yet to be fully explored. Here we report a global antagonistic effect on gene expression between two alternative σ factors, σN (RpoN) and σS (RpoS), a σD family protein. Mutations in rpoS and rpoN inversely affected a number of cellular traits, such as expression of flagellar genes, σN-controlled growth on poor nitrogen sources, and σS-directed expression of acid phosphatase AppA. Transcriptome analysis reveals that 40% of genes in the RpoN regulon were under reciprocal RpoS control. Furthermore, loss of RpoN led to increased levels of RpoS, while RpoN levels were unaffected by rpoS mutations. Expression of the flagellar σF factor (FliA), another σD family protein, was controlled positively by RpoN but negatively by RpoS. These findings unveil a complex regulatory interaction among σN, σS and σF, and underscore the need to employ systems biology approaches to assess the effect of such interaction of σ factors on cellular functions, including motility, nutrient utilization, and stress response. Precise deletion mutants of rpoS or rpoN of MG1655 were constructed and employed in this study. Cultures were inoculated in triplicate in M9 minimal media (0.2% glucose) at a starting OD of 0.0001 and grown aerobically at 37C. Cultures were harvested at OD600 = 0.3 in exponential phase. For RNA extraction, cultures were mixed directly with a boiling lysis buffer containing SDS and EDTA followed by acidic hot phenol to minimize RNA degradation. RNA samples were hybridized to Affymetrix E. coli Genome 2.0 Array according to Affymetrix's standard protocols.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-20095
refinement:
raw
alternateIdentifiers:
20095
keywords:
functional genomics
dateModified:
06-10-2011
availability:
available
types:
gene expression
name:
Escherichia coli K-12
ID:
A-AFFY-56
name:
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-20095/E-GEOD-20095.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-20095/E-GEOD-20095.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=GSE20095
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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