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RNA proximity labeling in log phase Caulobacter crescentus NA1000

ABSTRACT: RNA proximity labeling in log phase Caulobacter crescentus NA1000

PROVIDER: PRJNA1266958 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33677910.fastq.gz	Fastqsanger.gz
	SRR33677911.fastq.gz	Fastqsanger.gz
	SRR33677912.fastq.gz	Fastqsanger.gz
	SRR33677913.fastq.gz	Fastqsanger.gz
	SRR33677914.fastq.gz	Fastqsanger.gz

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RNA proximity labeling in log phase Caulobacter crescentus NA1000

Project description:APEX2 RNA proximity labeling is a powerful method for determining localized RNAs in vivo. APEX2 RNA proximity labeling was adapted to bacterial cells, using an APEX2 fusion to the core scaffold of BR-bodies, RNase E. As a control, APEX2 was also fused to a variant of RNase E that lacks its C-terminal IDR and is unable to form BR-bodies, RNase E delta CTD. RNA proximity labeling was performed, and we observed a similar pattern of enriched RNAs to density centrifugation isolated BR-bodies (Al-Husini et al. Mol Cell 2020).

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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.

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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

Expression analysis of Caulobacter crescentus NA1000 bearing a CCNA_00690 (cdnL) deletion [dcdnL] vs Caulobacter crescentus NA1000 wild type [wt]

Project description:Investigation of whole genome gene expression level changes in a Caulobacter crescentus NA1000 dcdnL mutant, compared to the wild-type strain. In bacteria, transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. Caulobacter crescentus cells lacking CdnL have severe morphological and growth defects. Our microarray experiment demonstrates how cdnL deletion affects the transcriptome of Caulobacter crescentus.

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

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BAP-seq proximity labeling of subcellular compartments

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Expression analysis of Caulobacter crescentus NA1000 bearing a CCNA_00690 (cdnL) deletion [dcdnL] vs Caulobacter crescentus NA1000 wild type [wt]

Project description:Expression analysis of Caulobacter crescentus NA1000 bearing a CCNA_00690 (cdnL) deletion [dcdnL] vs Caulobacter crescentus NA1000 wild type [wt]

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

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