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| Status |
Public on Jun 07, 2023 |
| Title |
The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development [ChIP-seq] |
| Organism |
Caulobacter vibrioides NA1000 |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
To investigate the NtrC direct regulon/DNA binding sites in Caulobacter by creating a 3xFLAG-tagged ntrC allele, which resulted in a 3xFLAG tag at the N-terminus of NtrC
We performed NtrC DNA-binding analysis from ChIP-seq data of Caulobacter harboring 3xFLAG-ntrC grown in PYE to log phase
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| Contributor(s) |
North H, McLaughlin M, Fiebig A, Crosson S |
| Citation(s) |
37791753 |
| |
| Submission date |
Jun 05, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Sean Crosson |
| E-mail(s) |
crosson4@msu.edu
|
| Phone |
5178845345
|
| Organization name |
Michigan State University
|
| Department |
Dept. Microbiology and Molecular Genetics
|
| Street address |
567 Wilson Rd
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL33463 |
NextSeq 2000 (Caulobacter vibrioides NA1000) |
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| Samples (2) |
| GSM7445764 |
∆ntrC xylX::pPTM057-3xFLAG-ntrC input DNA |
| GSM7445765 |
∆ntrC xylX::pPTM057-3xFLAG-ntrC output DNA |
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| This SubSeries is part of SuperSeries: |
| GSE234097 |
The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development |
|
| Relations |
| BioProject |
PRJNA980111 |
