E-MTAB-2211 - Nitrogen regulatory protein C couples nitrogen stress response and stringent response in nitrogen starved Escherichia coli

Released on 1 May 2014, last updated on 24 February 2016
Escherichia coli str. K-12 substr. MG1655
Samples (6)
Protocols (4)
We show that NtrC couples the Ntr stress response and stringent response in N starved E. coli, which appears to be a conserved adaptive strategy employed by many bacteria to manage conditions of nutritional adversity. N starved Escherichia coli initiate the nitrogen regulation (Ntr) stress response as an adaptive mechanism to scavenge for alternative N sources. The Ntr stress response requires the global transcriptional regulator nitrogen regulatory protein C (NtrC). We discovered that the transcription of relA, the key gene responsible for the synthesis of the major effector nucleotide alamorne of the bacterial stringent response, guanosine pentaphosphate (ppGpp), is positively regulated by NtrC in N starved E. coli. we addressed Ntr stress response-ppGpp alarmone links and mapped the genome-wide binding targets of NtrC in E. coli during N starvation using chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) to gain insight into the NtrC-dependent gene networks. To identify candidate genome regions that are preferentially associated with NtrC, we introduced an in-frame fusion encoding three repeats of the FLAG epitope to the 3-prime end of glnG in E. coli strain NCM3722, a prototrophic E. coli K-12 strain.
Experiment types
ChIP-seq, ChiP-seq, growth condition design, reference design
Nitrogen stress response and stringent response are coupled in Escherichia coli. Brown DR, Barton G, Pan Z, Buck M, Wigneshweraraj S. Nat Commun 5:4115 (2014), Europe PMC 24947454
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-2211.idf.txt
Sample and data relationshipE-MTAB-2211.sdrf.txt