DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus
Ontology highlight
ABSTRACT:
ORGANISM(S): Caulobacter vibrioides
PROVIDER: GSE3171 | GEO | 2005/12/08
SECONDARY ACCESSION(S): PRJNA92711
REPOSITORIES: GEO
Similar Datasets
Project description:DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus
| PRJNA92711 | ENA
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
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.
2014-01-08 | GSE52722 | GEO
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
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.
2014-01-08 | GSE52375 | GEO
Project description:This a model from the article:
A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells.
Shenghua Li, Paul Brazhnik, Bruno Sobral, John J. Tyson PLoS Comput Biol
2008 Jan 25:4(1): e9 18225942
,
Abstract:
Progression of a cell through the division cycle is tightly controlled at different steps to ensure the integrity of genome
replication and partitioning to daughter cells. From published experimental evidence, we propose a molecular
mechanism for control of the cell division cycle in Caulobacter crescentus. The mechanism, which is based on the
synthesis and degradation of three ‘‘master regulator’’ proteins (CtrA, GcrA, and DnaA), is converted into a quantitative
model, in order to study the temporal dynamics of these and other cell cycle proteins. The model accounts for
important details of the physiology, biochemistry, and genetics of cell cycle control in stalked C. crescentus cell. It
reproduces protein time courses in wild-type cells, mimics correctly the phenotypes of many mutant strains, and
predicts the phenotypes of currently uncharacterized mutants. Since many of the proteins involved in regulating the
cell cycle of C. crescentus are conserved among many genera of a-proteobacteria, the proposed mechanism may be
applicable to other species of importance in agriculture and medicine.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2018-11-07 | BIOMD0000000718 | BioModels
Project description:Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the first use of Hi-C to map the structure of bacterial chromosomes at a high, unprecedented resolution. Analysis of Hi-C data and polymer modeling indicates that the Caulobacter crescentus chromosome consists of multiple, largely independent spatial domains likely comprised of supercoiled plectonemes arrayed into a bottlebrush-like fiber. These domains are stable throughout the cell cycle and re-established concomitantly with DNA replication. We provide strong evidence that domain boundaries are established by highly-expressed genes and the formation of plectoneme-free regions. Additionally, we use Hi-C to demonstrate that supercoiling, the histone-like protein HU, and SMC act at different length-scales and in complementary ways to organize and structure chromosomes within cells. Hi-C experiments were performed on untreated wild type swarmer cells and drug-treated swarmer cells (Novobiocin or Rifampicin) of Caulobacter crescentus CB15N. Hi-C were also performed on swarmer cells of smc knock-out and hup1hup2 knock-out mutants of Caulobacter crescentus. Time-course Hi-C were performed on a synchronous population of Caulobacter crescentus at 5, 10, 30, 45, 60 and 75 minutes after synchronization. The progression of DNA replication during the cell cycle was followed by total genomic DNA sequencing.
2013-10-30 | E-GEOD-45966 | biostudies-arrayexpress
Project description:In α-proteobacteria, strict regulation of cell cycle progression is necessary for the specific cellular differentiation required for adaptation to diverse environmental niches. The symbiotic lifestyle of Sinorhizobium meliloti requires a drastic cellular differentiation that includes genome amplification. To achieve polyploidy, the S. meliloti cell cycle program must be altered to uncouple DNA replication from cell division. In the α-proteobacterium Caulobacter crescentus, cell cycle regulated transcription plays an important role in control of cell cycle progression but this has not been demonstrated in other α-proteobacteria. Here we describe a robust method for synchronizing cell growth that enabled the first global analysis of S. meliloti cell cycle regulated gene expression. The objective of the microarray-based cell cycle gene expression analysis was to determine which genes were transcriptionally regulated as a funciton of a cell cycle in order to understand the contribution of transcriptional regulation to the timing of cell cycle events. The microarray analysis identified 462 genes with cell cycle regulated transcripts, including several key cell cycle regulators, and genes involved in motility, attachment, and cell division. Only 28% of the 462 S. meliloti cell cycle regulated genes were also transcriptionally cell cycle regulated in C. crescentus. Furthermore, CtrA and DnaA binding motif analysis revealed little overlap between the cell cycle-dependent regulons of CtrA and DnaA in S. meliloti and C. crescentus. The predicted S. meliloti cell cycle regulon of CtrA, but not that of DnaA, was strongly conserved in more closely related α-proteobacteria with similar ecological niches as S. meliloti, suggesting that the CtrA cell cycle regulatory network may control functions of central importance to the specific lifestyles of α-proteobacteria. Gene expression levels were quantified in synchronously growing S. meliloti cultures across 8 time points and compared to gene expression levels in unsynchronized culture via a two-color custom agilent array
2014-01-22 | GSE54208 | GEO
Project description:In α-proteobacteria, strict regulation of cell cycle progression is necessary for the specific cellular differentiation required for adaptation to diverse environmental niches. The symbiotic lifestyle of Sinorhizobium meliloti requires a drastic cellular differentiation that includes genome amplification. To achieve polyploidy, the S. meliloti cell cycle program must be altered to uncouple DNA replication from cell division. In the α-proteobacterium Caulobacter crescentus, cell cycle regulated transcription plays an important role in control of cell cycle progression but this has not been demonstrated in other α-proteobacteria. Here we describe a robust method for synchronizing cell growth that enabled the first global analysis of S. meliloti cell cycle regulated gene expression. The objective of the microarray-based cell cycle gene expression analysis was to determine which genes were transcriptionally regulated as a funciton of a cell cycle in order to understand the contribution of transcriptional regulation to the timing of cell cycle events. The microarray analysis identified 462 genes with cell cycle regulated transcripts, including several key cell cycle regulators, and genes involved in motility, attachment, and cell division. Only 28% of the 462 S. meliloti cell cycle regulated genes were also transcriptionally cell cycle regulated in C. crescentus. Furthermore, CtrA and DnaA binding motif analysis revealed little overlap between the cell cycle-dependent regulons of CtrA and DnaA in S. meliloti and C. crescentus. The predicted S. meliloti cell cycle regulon of CtrA, but not that of DnaA, was strongly conserved in more closely related α-proteobacteria with similar ecological niches as S. meliloti, suggesting that the CtrA cell cycle regulatory network may control functions of central importance to the specific lifestyles of α-proteobacteria. Gene expression levels were quantified in synchronously growing S. meliloti cultures across 8 time points and compared to gene expression levels in unsynchronized culture via a two-color custom agilent array A two-color array format was used with time point from synchronous culture being competed with a sample from unsynchronized culture (control same for all arrays) to determine the cell cycle-phase specific induction or repression of genes relative to batch culture which contains cells in all phases of the cell cycle. For each of the 8 cell cycle time points, four biological replicates were used resulting in 4 arrays per time point and a total of 32 arrays. The arrays also contained duplicates of each probe resulting in two technical replicates per biological replicate per time point.
2014-01-22 | E-GEOD-54208 | biostudies-arrayexpress
Project description:Cell cycle progression requires the coordination of cell growth, chromosome replication, and division. Consequently, a functional cell cycle must be coupled with metabolism. However, direct measurements of metabolome dynamics remained scarce, in particular in bacteria. Here, we describe an untargeted metabolomics approach with synchronized Caulobacter crescentus cells to monitor the relative abundance changes of ~400 putative metabolites as a function of the cell cycle. While the majority of metabolite pools remains homeostatic, ~14% respond to cell cycle progression. In particular, sulfur metabolism is redirected during the G1-S transition, and glutathione levels periodically change over the cell cycle with a peak in late S phase. A lack of glutathione perturbs cell size by uncoupling cell growth and division through dysregulation of KefB, a K+/H+ antiporter. Overall, we here describe the impact of the C. crescentus cell cycle progression on metabolism, and in turn relate glutathione and potassium homeostasis to timely cell division.
2020-10-15 | MTBLS1402 | MetaboLights