Ontology highlight
ABSTRACT:
PROVIDER: PRJNA670525 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12873941_1.fastq.gz | Fastqsanger.gz | |||
| SRR12873941_2.fastq.gz | Fastqsanger.gz | |||
| SRR12873942_1.fastq.gz | Fastqsanger.gz | |||
| SRR12873942_2.fastq.gz | Fastqsanger.gz |
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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:Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions. In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress. The molecular reasons underlying Hsp70 essentiality remain in most cases unclear. Here, we demonstrate that DnaK is essential in the α-proteobacterium Caulobacter crescentus due to its regulatory function in gene expression. Using a suppressor screen we identified mutations in genes coding for different components of the transcriptional machinery as well as an ATP dependent protease that allow growth in the absence of DnaK. These mutations reduced the activity of the heat shock sigma factor σ32 by different mechanisms, suggesting that DnaK's sole essential function in the absence of stress is the inactivation of σ32. We found that σ32 inhibits growth and that its unleashed activity leads to an extensive reprogramming of global gene expression, which re-allocates cellular resources from proliferative to maintenance functions. While this re-allocation provides an advantage during heat stress, it leads to detrimental growth defects under favorable conditions. We conclude that Caulobacter has co-opted the DnaK chaperone system as an essential regulator of gene expression under conditions when its folding activity is dispensable.
2017-12-13 | GSE102372 | GEO
Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism. An allele of phoB bearing a C-terminal 3x-flag tag was integrated at its native locus, and ChIP followed by deep sequencing on Illumina MiSeq was performed on samples grown in rich medium, phosphate-limited medium, and in a pstS::Tn5 mutant background in rich medium.
2016-08-06 | E-GEOD-71860 | biostudies-arrayexpress
Project description:genome re-sequencing of suppressor mutants of ptr1-1
| PRJDB1937 | ENA
Project description:Proper chromosome segregation is essential in all living organisms if daughter cells are each to inherit a full copy of genetic information. In Caulobacter crescentus, the ParA-ParB-parS system is required for proper chromosome segregation and cell viability. The bacterial centromere-like parS DNA locus is the first to be segregated following chromosome replication. parS is recognized and bound by ParB protein, which in turn interacts with ParA to partition the ParB-parS nucleoprotein complex to each daughter cell. In this study, we investigated the genome-wide distribution of ParB on the Caulobacter chromosome using a combination of in vivo chromatin immunoprecipitation (ChIP-seq) and in vitro DNA affinity purification with deep sequencing (IDAP-seq). We confirmed two previously identified parS sites and discovered at least three more sites that cluster ~8 kb from the origin of replication. We showed that Caulobacter ParB nucleates at parS sites, then associates non-specifically with flanking DNA to form a high-order nucleoprotein complex that occupies an extensive ~10 kb DNA segment on the left chromosomal arm. Lastly, using transposon mutagenesis coupled with deep sequencing (Tn-seq), we identified a ~500 kb region surrounding the origin of replication and a ~100 kb region surrounding the terminus of the Caulobacter chromosome that are tolerable to the insertion of a second parS cluster without severely affecting cell viability. Our results demonstrate that the genomic distribution of the bacterial centromere-like parS is highly restricted and is crucial for chromosome segregation in Caulobacter.
2017-08-09 | GSE100233 | GEO
Project description:Caulobacter sp. YL-Caulobacter Genome sequencing
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Project description:We report that ancestral zinc-finger-domain transcriptional regulators, previously reported to control virulence/symbiosis, implement a cell cycle (SM-bM-^FM-^RG1) transcriptional switch. To unravel how this G1-phase transcriptional program is reinstated during a primitive cell cycle, we first defined G1-specific promoters in the model bacterium Caulobacter crescentus by comparative ChIP-Seq analysis. We then exploited one such promoter as genetic proxy, to identify two conserved developmental regulator paralogs, MucR1/2, that constitute a quadripartite and homeostatic regulatory module directing the switch from SM-bM-^FM-^RG1-phase transcription. Surprisingly, MucR orthologs that regulate virulence and symbiosis gene transcription in Brucella, Agrobacterium or Sinorhizobium support the G1 transcriptional switch in Caulobacter. Pan-genomic ChIP-Seq analyses in Sinorhizobium and Caulobacter show that this module targets orthologous genes. Thus, this ancestral bacterial lineage from which eukaryotic organelles descended may coordinate virulence/symbiosis with other cell cycle functions using a primordial transcription factor fold that is now primarily found in the eukaryotic domain of life. Examination of 5 transcripton factor binding in two different species
2014-05-25 | E-GEOD-52849 | biostudies-arrayexpress
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
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