Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Nitrogen regulatory protein C couples nitrogen stress response and stringent response in nitrogen starved Escherichia coli.

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Barton Geraint

PROVIDER: E-MTAB-2211 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Nitrogen stress response and stringent response are coupled in Escherichia coli.

Brown Daniel R DR Barton Geraint G Pan Zhensheng Z Buck Martin M Wigneshweraraj Sivaramesh S

Nature communications 20140620

Assimilation of nitrogen is an essential process in bacteria. The nitrogen regulation stress response is an adaptive mechanism used by nitrogen-starved Escherichia coli to scavenge for alternative nitrogen sources and requires the global transcriptional regulator NtrC. In addition, nitrogen-starved E. coli cells synthesize a signal molecule, guanosine tetraphosphate (ppGpp), which serves as an effector molecule of many processes including transcription to initiate global physiological changes, c ...[more]

PMID: 24947454

Similar Datasets

Project description:Caulobacter species are dimorphic Gram-negative bacteria that inhabit diverse terrestrial and aquatic ecosystems. A suite of molecular sensory systems enables these microbes to control growth, development, and reproduction in response to levels of essential elements, including carbon, nitrogen, and phosphorus. Although the enhancer binding protein NtrC and its cognate sensor histidine kinase NtrB are well-established regulators of bacterial nitrogen assimilation, their precise functions in Caulobacter metabolism and cell development remained largely undefined. Deletion of C. crescentus ntrC slowed cell growth in complex medium, while ntrB and ntrC were essential for growth when ammonium was the sole nitrogen source due to their requirement for glutamine synthase (glnA) expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring glnBA transcription, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nitrogen limitation. We further defined the NtrC regulon through transcriptomic and ChIP-seq analyses, which demonstrated the role of NtrC as both a transcriptional activator and repressor. The chromosome of C. crescentus harbors dozens of direct binding sites for NtrC, with a significant proportion located near genes involved in polysaccharide biosynthesis. Numerous NtrC binding sites align with those of GapR, an essential protein involved in chromosome organization, and MucR1, a cell cycle regulator. This observation suggests that NtrC participates in the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. These developmental defects were restored by supplementing media with glutamine or by ectopic expression of the glnBA operon. This study establishes a regulatory connection between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter.

Dataset Information

Nitrogen regulatory protein C couples nitrogen stress response and stringent response in nitrogen starved Escherichia coli.

Publications

Nitrogen stress response and stringent response are coupled in Escherichia coli.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure