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The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle [mapping]

ABSTRACT: The Caulobacter cell cycle includes in an asymmetric cell division that is driven by a core regulatory circuit comprised of 4 transcription factors (DnaA, GcrA, CtrA, and SciP) and a DNA methyltransferase (CcrM). Using a modified global 5M-bM-^@M-^Y RACE protocol we mapped 2,726 transcriptional start sites (TSS) in the 4mb Caulobacter genome and identified 586 cell cycle-regulated TSS. The core cell cycle circuit directly controls about 55% of cell cycle-regulated TSS by integrating multiple regulatory inputs within at least 322 promoters, providing a large number of transcription profiles from a small number of regulatory factors. Here, we identified previously unknown features of the core cell cycle circuit, including antisense TSS within dnaA and ctrA, plus newly identified TSS for ctrA and ccrM. Altogether, we identified 615 antisense TSS plus 241 genes that are transcribed from multiple TSS. The multiple TSS in the same promoter region often exhibit different cell cycle activation timing, These novel features of the global transcript profile add significant insight to the system architecture of the Caulobacter cell cycle regulatory circuit. Global 5' RACE was performed to map Transcription Start Sites in the Caulobacter NA1000 genome

ORGANISM(S): Caulobacter crescentus NA1000

SUBMITTER: Jared Schrader

PROVIDER: E-GEOD-57365 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle [timecourse]

Project description:The Caulobacter cell cycle includes in an asymmetric cell division that is driven by a core regulatory circuit comprised of 4 transcription factors (DnaA, GcrA, CtrA, and SciP) and a DNA methyltransferase (CcrM). Using a modified global 5M-bM-^@M-^Y RACE protocol we mapped 2,726 transcriptional start sites (TSS) in the 4mb Caulobacter genome and identified 586 cell cycle-regulated TSS. The core cell cycle circuit directly controls about 55% of cell cycle-regulated TSS by integrating multiple regulatory inputs within at least 322 promoters, providing a large number of transcription profiles from a small number of regulatory factors. Here, we identified previously unknown features of the core cell cycle circuit, including antisense TSS within dnaA and ctrA, plus newly identified TSS for ctrA and ccrM. Altogether, we identified 615 antisense TSS plus 241 genes that are transcribed from multiple TSS. The multiple TSS in the same promoter region often exhibit different cell cycle activation timing, These novel features of the global transcript profile add significant insight to the system architecture of the Caulobacter cell cycle regulatory circuit. Global 5' RACE was performed to measure Transcription Start Site activity at time points of the Caulobacter NA1000 cell cycle

2014-10-16 | E-GEOD-57364 | biostudies-arrayexpress

The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle [mapping]

Project description:The Caulobacter cell cycle includes in an asymmetric cell division that is driven by a core regulatory circuit comprised of 4 transcription factors (DnaA, GcrA, CtrA, and SciP) and a DNA methyltransferase (CcrM). Using a modified global 5’ RACE protocol we mapped 2,726 transcriptional start sites (TSS) in the 4mb Caulobacter genome and identified 586 cell cycle-regulated TSS. The core cell cycle circuit directly controls about 55% of cell cycle-regulated TSS by integrating multiple regulatory inputs within at least 322 promoters, providing a large number of transcription profiles from a small number of regulatory factors. Here, we identified previously unknown features of the core cell cycle circuit, including antisense TSS within dnaA and ctrA, plus newly identified TSS for ctrA and ccrM. Altogether, we identified 615 antisense TSS plus 241 genes that are transcribed from multiple TSS. The multiple TSS in the same promoter region often exhibit different cell cycle activation timing, These novel features of the global transcript profile add significant insight to the system architecture of the Caulobacter cell cycle regulatory circuit.

2014-10-16 | GSE57365 | GEO

The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle [timecourse]

Project description:The Caulobacter cell cycle includes in an asymmetric cell division that is driven by a core regulatory circuit comprised of 4 transcription factors (DnaA, GcrA, CtrA, and SciP) and a DNA methyltransferase (CcrM). Using a modified global 5’ RACE protocol we mapped 2,726 transcriptional start sites (TSS) in the 4mb Caulobacter genome and identified 586 cell cycle-regulated TSS. The core cell cycle circuit directly controls about 55% of cell cycle-regulated TSS by integrating multiple regulatory inputs within at least 322 promoters, providing a large number of transcription profiles from a small number of regulatory factors. Here, we identified previously unknown features of the core cell cycle circuit, including antisense TSS within dnaA and ctrA, plus newly identified TSS for ctrA and ccrM. Altogether, we identified 615 antisense TSS plus 241 genes that are transcribed from multiple TSS. The multiple TSS in the same promoter region often exhibit different cell cycle activation timing, These novel features of the global transcript profile add significant insight to the system architecture of the Caulobacter cell cycle regulatory circuit.

2014-10-16 | GSE57364 | GEO

Bypass of an epigenetic S-phase transcriptional module by convergent nutrient stress signals

Project description:The signals feeding into bacterial S-phase transcription are poorly understood. Cellular cycling in the alpha-proteobacterium Caulobacter crescentus is driven by a complex circuit of at least three transcriptional modules that direct sequential promoter firing during the G1, early and late S cell cycle phases. In alpha-proteobacteria, the transcriptional regulator GcrA and the CcrM methyltransferase epigenetically activate promoters of cell division and polarity genes that fire in S-phase. By evolving Caulobacter crescentus cells to cycle and differentiate in the absence of the GcrA/CcrM module, we discovered that phosphate deprivation and (p)ppGpp alarmone stress signals converge on S-phase transcriptional activation. The cell cycle oscillations of the CtrA protein, the transcriptional regulator CtrA that implements G1 and late S-phase transcription, are essential in our evolved mutants, but not in wild-type cells, showing that the periodicity in CtrA abundance alone can sustain cellular cycling without GcrA/CcrM. While similar nutritional sensing occurs in other alpha-proteobacteria, GcrA and CcrM are not encoded in the reduced genomes of obligate intracellular relatives. We thus propose that the nutritional stress response induced during intracellular growth obviated the need for an S-phase transcriptional regulator.

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SMORE-seq maps both ends of transcripts and identifies widespread promoter-associated non-coding RNA governed by TATA elements.

Project description:SMORE-seq (Simultaneous Mapping Of RNA Ends by sequencing) is developted to simultaneously identify the strongest TSS (Transcription Start Site) and PAS (Polyadenylation Site) SMORE-seq were performed in wild type Saccharomyces cerevisiae

2014-02-04 | E-GEOD-49026 | biostudies-arrayexpress

sciP array data

2010-12-01 | GSE22062 | GEO

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

sciP array data

Project description:Progression through the Caulobacter cell cycle is driven by the master regulator CtrA, an essential two-component signaling protein that regulates the expression of nearly 100 genes. CtrA is abundant throughout the cell cycle except immediately prior to DNA replication. However, the expression of CtrA-activated genes is generally restricted to S-phase. We identify the conserved protein SciP (small CtrA inhibitory protein) and show that it accumulates during G1 where it inhibits CtrA from activating target genes. The depletion of SciP from G1 cells leads to the inappropriate induction of CtrA-activated genes and, consequently, a disruption of the cell cycle. Conversely, the ectopic synthesis of SciP is sufficient to inhibit CtrA-dependent transcription, also disrupting the cell cycle. SciP binds directly to CtrA without affecting stability or phosphorylation; instead SciP likely prevents CtrA from recruiting RNA polymerase. CtrA is thus tightly regulated by a protein-protein interaction which is critical to cell cycle progression. For the sciP depletion studies, the sciP depletion strain was grown to mid-exponential phase in rich media supplemented with xylose, synchronized, and swarmer cells released into either glucose or xylose. Following one cell cycle, swarmers were again isolated from the two conditions and compared directly on arrays. This was done in duplicate. For the sciP overexpression studies, a wild type strain harboring the plasmid pJS14-Pxyl-sciP was grown to mid-exponential phase and xylose added for 2 hours. A strain harboring an empty vector was treated identically. The two populations were compared directly on arrays. This was done in duplicate.

2010-12-01 | E-GEOD-22062 | 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

Developmental switch within the bacterial cell cycle regulator CtrA

Project description:Many bacteria acquire dissemination and virulence traits in G1-phase. CtrA, an essential and conserved cell cycle transcriptional regulator identified in the dimorphic alpha-proteobacterium Caulobacter crescentus, mysteriously switches from activating promoters in late S-phase to a different set in G1-phase. We found that a core and highly conserved determinant in the DNA-binding domain (DBD) of CtrA governs this promoter switch and that it is also required for promoter reprogramming in stationary phase in response to a (p)ppGpp alarmone signal perceived by the RNA polymerase beta subunit. A simple side chain modification in one critical residue of this DBD confers opposing developmental phenotypes and transcriptional activities. This region is also central to understanding the developmental reprogramming in the obligate intracellular Rickettsiae where replicative cells develop into dispersal cells and a naturally occurring polymorphism in the rickettsial DBD resembles a mutation that drives CtrA towards activation of the dispersal (G1-phase) program in Caulobacter.

2019-11-25 | GSE134017 | GEO

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