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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from Caulobacter crescentus (syn. C. vibrioides) swarmer and stalked cells starved for carbon

ABSTRACT: Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of specific developmental stages of C. crescentus -swarmer and stalked cells- to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis. Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures, and total RNA was extracted after 30 and 60 minutes of incubation. The controls are cells growing in complete media.

ORGANISM(S): Caulobacter vibrioides

SUBMITTER: Leticia Britos

PROVIDER: E-GEOD-25997 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from Caulobacter crescentus starved for carbon

2011-04-20 | E-GEOD-25996 | biostudies-arrayexpress

Expression data from WT, DSigT and DSigU Caulobacter crescentus (syn. C. vibrioides) starved for carbon

Project description:Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of C. crescentus to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis. We explored the differential gene expression changes in wild type cells and cells carrying deletions of two alternative extracytoplasmic function sigma factors, SigT and SigU. Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures (wild-type (strain LS101), DSigT (strain LS3554) and DSigU (strain LS3547)). Total RNA was extracted after 15 minutes of incubation. Controls are cells that were mock washed and incubated in parallel in complete media.

2011-04-20 | E-GEOD-25998 | biostudies-arrayexpress

Caulobacter crescentus starved for carbon

Project description:This SuperSeries is composed of the following subset Series: GSE25996: Expression data from Caulobacter crescentus starved for carbon GSE25997: Expression data from Caulobacter crescentus (syn. C. vibrioides) swarmer and stalked cells starved for carbon GSE25998: Expression data from WT, DSigT and DSigU Caulobacter crescentus (syn. C. vibrioides) starved for carbon Refer to individual Series

2011-04-20 | E-GEOD-25999 | biostudies-arrayexpress

Comparing the transcriptional profiles of a Caulobacter crescentus CB15N (NA1000) wild-type to a SpoT null in carbon starvation.

Project description:SpoT is an Rsh (Rel / Spo homolog) protein, which synthesizes the alarmone ppGpp in response to starvation. This experiment is quantifying transcription in two Caulobacter strains after 5 minutes of glucose starvation: one strain is wild-type CB15N (NA1000); the other strain is NA1000 which has a chromosomal in-frame deletion of the spoT gene. The wild-type strain can synthesize the alarmone ppGpp in response to starvation and the spoT null strain cannot. Both strains were cultured in M2 defined medium with glucose as the sole carbon source, and then washed and incubated in M2 medium lacking glucose for 5 minutes before RNA isolation. Triplicate cultures of: 1) C. crescentus strain CB15N , and 2) CB15N ?SpoT, cultured in M2-glucose media, then starved for glucose for 5 minutes.

2011-05-01 | E-GEOD-21206 | biostudies-arrayexpress

Expression analysis of Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) [DccrM] vs Caulobacter crescentus NA1000 wild type [WT]

Project description:Investigation of whole genome gene expression level changes in a Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain render it incapable of methylating its genome on the adenine at GANTC motifs. References for strains : WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. DccrM: Gonzalez, D. and Collier, J. (2013) DNA methylation by CcrM activates the transcription of two genes required for the division of Caulobacter crescentus. Mol Microbiol, 88, 203-218. A six chip study using total RNA recovered from three separate wild-type cultures of Caulobacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive. Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.

2014-01-08 | E-GEOD-52375 | biostudies-arrayexpress

Caulobacter strains ET163 and ET166 vs. CB15N (wild-type)

Project description:The goal of this study was to compare the expression profiles of inversion strains ET163 and ET166 to that of wild-type. To this end we performed transcriptional profiling of Caulobacter crescentus swarmer cells from strains ET163, ET166, and CB15N (WT). Two strain experiment. ET163 vs. WT and ET166 vs. WT. Biological replicates: 2 ET163, 2 ET166, and 3 Wild-type

2011-12-01 | E-GEOD-31468 | biostudies-arrayexpress

Expression analysis of Caulobacter crescentus NA1000 Plac::CCNA_00382 (ccrM) vs Caulobacter crescentus

Project description:Investigation of whole genome gene expression level changes in a Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain cause the CcrM DNA methyltransferase to be overexpressed and the chromosome to be constitutively methylated at the adenine at GANTC motifs. References of strains: CcrMOE: Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. A six chip study using total RNA recovered from three separate wild-type cultures of Caulonacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive. Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.

2014-01-08 | E-GEOD-52722 | biostudies-arrayexpress

HipBA toxin-antitoxin system Caulobacter crescentus.

Project description:Antibiotic persistence is a transient phenotypic state during which a bacterium can withstand otherwise lethal antibiotic exposure or environmental stresses. In Escherichia coli, persistence is promoted by the HipBA toxin-antitoxin system. The HipA toxin functions as a serine/threonine kinase that inhibits cell growth, while the HipB antitoxin neutralizes the toxin. E. coli HipA inactivates the glutamyl-tRNA synthetase GltX, which inhibits translation and triggers the highly conserved stringent response. Although hipBA operons are widespread in bacterial genomes, it is unknown if this mechanism is conserved in other species. Here we describe the functions of three hipBA modules in the alpha-proteobacterium Caulobacter crescentus. The HipA toxins have different effects on growth and macromolecular syntheses, and they phosphorylate distinct substrates. HipA1 and HipA2 contribute to antibiotic persistence during stationary phase by phosphorylating the aminoacyl-tRNA synthetases GltX and TrpS. The stringent response regulator SpoT is required for HipA-mediated antibiotic persistence, but persister cells can form in the absence of all hipBA operons or spoT, indicating that multiple pathways lead to persister cell formation in C. crescentus.

2020-02-06 | PXD015525 | Pride

Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus

Project description:Bacteria use a range of small signaling molecules to tune their physiology in response to changes in the environment. It has remained unclear if these regulatory networks operate independently or if they interact to optimize bacterial growth and survival. Here, we demonstrate that (p)ppGpp and c-di-GMP reciprocally regulate growth of Caulobacter crescentus by converging on a single small-molecule-binding protein, SmbA. Both second messengers bind to SmbA with high affinity and in a competitive manner, with the guanine moiety of (p)ppGpp and one of the guanyl bases of dimeric c-di-GMP forming identical interactions with SmbA. While c-di-GMP binding inhibits SmbA, (p)ppGpp interferes with this inhibition to sustain SmbA activity. We demonstrate that (p)ppGpp specifically promotes Caulobacter growth on glucose, while c-di-GMP inhibits glucose consumption. We find that SmbA contributes to this metabolic switch and promotes growth on glucose by quenching redox stress under these conditions. The identification of the first effector protein that acts as a central regulatory hub for two global second messengers opens up future studies on specific cross-talk between small-molecule-based regulatory networks.

2020-12-08 | PXD019846 | Pride

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

Project description:We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. Gene and module co-expression clustering reveal co-regulated pathways and suggest functionally coupled genes. In addition, an evolutionary analysis of the cell cycle network shows a high correlation between co-expression and co-evolution. Most co-expression modules have strong phylogenetic signals, with broadly conserved genes and clade-specific genes predominating different substructures of the cell cycle co-expression network. We also found that conserved genes tend to determine the expression profile of their module. We describe the first phylogenetic and single-nucleotide-resolution transcriptomic analysis of a bacterial cell cycle network. In addition, the study suggests how evolution has shaped this network and provides direct biological network support that selective pressure is not on individual genes but rather on the relationship between genes, which highlights the importance of integrating phylogenetic analysis into biological network studies. Examination of 5 typical cell cycle types (5 samples), each with 3 biological replicates

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