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E-GEOD-20095 - Antagonistic regulation of motility and other cellular functions by RpoN and RpoS in Escherichia coli

Status
Released on 4 December 2010, last updated on 10 June 2011
Organism
Escherichia coli K-12
Samples (9)
Array (1)
Protocols (7)
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.
Experiment type
transcription profiling by array 
Contacts
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-20095.idf.txt
Sample and data relationshipE-GEOD-20095.sdrf.txt
Processed data (1)E-GEOD-20095.processed.1.zip
Array designA-AFFY-56.adf.txt
Links