The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development [RNA-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA980100 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24827410_1.fastq.gz | Fastqsanger.gz | |||
| SRR24827410_2.fastq.gz | Fastqsanger.gz | |||
| SRR24827411_1.fastq.gz | Fastqsanger.gz | |||
| SRR24827411_2.fastq.gz | Fastqsanger.gz | |||
| SRR24827412_1.fastq.gz | Fastqsanger.gz |
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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.
2023-06-07 | GSE234096 | GEO
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.
2023-06-07 | GSE234095 | GEO
Project description:The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development
| PRJNA980102 | ENA
Project description:The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development [ChIP-seq]
| PRJNA980111 | ENA
Project description:A suite of molecular sensory systems enables Caulobacter to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer binding protein (bEBP) NtrC, and its cognate sensor histidine kinase NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in Caulobacter metabolism and development are not well defined. Notably, Caulobacter NtrC is an unconventional bEBP that lacks the σ54-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of C. crescentus ntrC slows cell growth in complex medium, and that ntrB and ntrC are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase (glnA) expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring transcription of the glnBA operon, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nutrient limitation. We further identified dozens of direct NtrC binding sites on the C. crescentus chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact 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. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter .
| S-EPMC10274813 | biostudies-literature
Project description:A suite of molecular sensory systems enables Caulobacter to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer-binding protein (bEBP) NtrC and its cognate sensor histidine kinase, NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in Caulobacter metabolism and development are not well defined. Notably, Caulobacter NtrC is an unconventional bEBP that lacks the σ54-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of Caulobacter crescentus ntrC slows cell growth in complex medium and that ntrB and ntrC are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring transcription of the glnBA operon, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nutrient limitation. We further identified dozens of direct NtrC-binding sites on the C. crescentus chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid-associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact 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. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter. IMPORTANCE Bacteria balance cellular processes with the availability of nutrients in their environment. The NtrB-NtrC two-component signaling system is responsible for controlling nitrogen assimilation in many bacteria. We have characterized the effect of ntrB and ntrC deletion on Caulobacter growth and development and uncovered a role for spontaneous IS element transposition in the rescue of transcriptional and nutritional deficiencies caused by ntrC mutation. We further defined the regulon of Caulobacter NtrC, a bacterial enhancer-binding protein, and demonstrate that it shares specific binding sites with essential proteins involved in cell cycle regulation and chromosome organization. Our work provides a comprehensive view of transcriptional regulation mediated by a distinctive NtrC protein, establishing its connection to nitrogen assimilation and developmental processes in Caulobacter.
| S-EPMC10601693 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-06-07 | GSE234097 | GEO
Project description:We have discovered an unusual two-tiered pattern of suppression in Caulobacter whereby temperature sensitive mutations in the "essential" cell cycle regulatory histidine kinase, CckA, are variably rescued by structurally distinct loss-of-function mutations in ntrC. NtrC regulates nitrogen assimilation and contains structural features that indicate interaction with σ70 RNA polymerase to control transcription. Considering that NtrC is a transcription factor, we hypothesized several mechanisms through which loss-of-function mutations in ntrC could rescue cckA(ts) conditional lethality through its effect on transcription: (a) ntrC mutations in a cckA(ts) background broadly restore Caulobacter gene expression to wild-type levels, (b) ntrC mutations shift gene expression into a state entirely distinct from both wild-type and the primary mutant, or (c) a combination of these two effects. To assess these models, we used RNA sequencing (RNA-seq) to measure the effect of shifting the cckA(ts) strain to the restrictive temperature and the global transcriptional impact of combining loss-of-function ntrC mutations with cckA(ts) at the restrictive temperature.
2025-01-03 | GSE285684 | GEO
Project description:Burkholderia cenocepacia is a versatile opportunistic pathogen that survives in a wide variety of environments, which can be limited in nutrients such as nitrogen. We previously showed that B. cenocepacia sigma factor s54 played a major role in control of nitrogen assimilation and virulence. In this work, we investigated the role of the s54 enhancer binding protein NtrC in controlling the response to nitrogen limitation and virulence. RNA-Seq analyses and phenotypical analysis on a ntrC mutant strain showed that, in addition to orchestrating uptake of nitrogen sources, NtrC is also regulating exopolysaccharide (EPS) production and motility. A search for NtrC consensus sequences identified a potential binding sequence in the promoter region of gene clusters involved in EPS formation and flagellar rotation suggesting that NtrC directly controls the expression of these phenotypic traits in B. cenocepacia H111.
2017-08-17 | GSE95607 | GEO
Project description:Azospirillum brasilense is a free-living diazothophic bacterium that associates with important grasses and cereals, promoting plant growth and increasing crop productivity. The nitrogen metabolism in this organism is tightly regulated by the availability of nitrogen and by the Ntr regulatory system. This system comprises the GlnD protein, which is capable of adding uridylyl groups to the PII proteins, GlnB and GlnZ, under limiting nitrogen levels. Under such conditions, the histidine kinase NtrB cannot interact with GlnB and phosphorylate NtrC. When phosphorylated, NtrC is a transcriptional activator of genes involved in metabolism of alternative nitrogen sources. Considering the key role of NtrC in nitrogen metabolism in Azospirillum brasilense, in this work we evaluated the proteomic and metabolomic profiles of the wild type FP2 strain and its mutant ntrC grown under high and low nitrogen. Analysis of the integrated data identifies, novel NtrC targets, including proteins involved in the response against oxidative stressnm (i.e., glutathione S-transferase and hydroperoxide resistance protein,), underlining the importance of NtrC to bacterial survival under oxidative stress conditions.
2019-10-14 | PXD014120 | Pride