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DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells

ABSTRACT: DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells

PROVIDER: PRJNA646729 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11638304.fastq.gz	Fastqsanger.gz
	SRR11638305.fastq.gz	Fastqsanger.gz
	SRR11638306.fastq.gz	Fastqsanger.gz
	SRR11638307.fastq.gz	Fastqsanger.gz
	SRR11638308.fastq.gz	Fastqsanger.gz

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DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells [2]

Project description:RNA-DNA hybrids form throughout the chromosome during normal cell growth and under stress conditions. When left unresolved, RNA-DNA hybrids can slow replication fork progression, cause DNA breaks, increase mutagenesis, and reduce gene expression. To remove hybrids, all organisms use ribonuclease H (RNase H) to specifically degrade the RNA portion of RNA-DNA hybrids. Here we show that, in addition to chromosomally encoded RNase HII and RNase HIII, Bacillus subtilis NCIB 3610 encodes a previously uncharacterized RNase HI protein, RnhP, on the endogenous plasmid pBS32. Like other RNase HI enzymes, RnhP incises Okazaki fragments, ribopatches, and a complementary RNA-DNA hybrid. We show that while chromosomally encoded RNase HIII is required for pBS32 hyper-replication, RnhP compensates for loss of RNase HIII activity on the chromosome. Consequently, loss of RnhP and RNase HIII impairs bacterial growth. We show that the decreased growth rate can be explained by laggard replication fork progression near the terminus region of the right replichore resulting in SOS-dependent inhibition of cell division. We conclude that B. subtilis NCIB 3610 encodes functional RNase HI, HII, and HIII, and pBS32-encoded RNase HI contributes to replication fork progression and chromosome stability while RNase HIII is important for chromosome stability and plasmid hyper-replication.

2020-07-16 | GSE154585 | GEO

DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells [1]

2020-04-30 | GSE149552 | GEO

DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells [2]

Project description:DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells [2]

| PRJNA646731 | ENA

DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells [1]

Project description:DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells [1]

| PRJNA629098 | ENA

RNA-seq of Bacillus subtilis wild type and RNase J1 null strains

Project description:RNase J1 is the first nuclease with 5-3 exonuclease activity in bacteria and plays an important role in the maturation and degradation of mRNA. Absence of RNase J1 in cells has effect on cell morphology and growth rate. We did RNA-seq of Bacillus subtilis wild type and RNase J1 null strains (triplicates) to obtain more information about cellular role of this nuclease in cells. Complmentary ChIP-seq data have also been deposited in ArrayExpress under accession number E-MTAB-5659 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5659 ).

2019-12-31 | E-MTAB-5660 | biostudies-arrayexpress

DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-07-16 | GSE154586 | GEO

RNA processing in Bacillus subtilis: Identification of targets of the essential RNase Y

2011-09-01 | GSE30430 | GEO

Comparison of wild-type Synechocystis sp. PCC 6803 with strains overexpressing wild-type or 5’-sensing-deficient RNase E

Project description:We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of different strains of the cyanobacterium Synechocystis sp. PCC6803. Comparison encompassed wild-type Synechocystis (WT), a strain overexpressing RNase E and RNase HII (rne(WT)) and a strain overexpressing 5’-sensing-deficient RNase E and RNase HII (rne(5p)). Analysis of changing 5'-monophosphorylated ends revealed 5’ sensing depedent processing sites on a transcriptome-wide level.

2023-01-20 | GSE184824 | GEO

RNA processing in Bacillus subtilis: Identification of targets of the essential RNase Y

Project description:RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the global impact of RNase Y, we compared the transcriptomes of strains expressing RNase Y or depleted for RNase Y. Our results indicate that processing by RNase Y results in accumulation of about 80 mRNAs. Some of these targets were substantially stabilized by RNase Y depletion, resulting in half-lives in the range of an hour. Moreover, about 40 mRNAs were less abundant when RNase Y was depleted among them the mRNAs of the operons required for biofilm formation. Interestingly, overexpression of RNase Y was sufficient to induce biofilm formation. The results emphasize the importance of RNase Y for B. subtilis and are in support of the idea that RNase Y is the functional equivalent of RNase E. To study the global function of RNase Y, a microarray analysis was performed with a B. subtilis strain allowing controlled depletion of RNase Y. Strain GP193 (Commichau et al., 2009, Mol. Cell. Proteomics 8: 1350-1360) expressing the rny gene under the control of a xylose-inducible promoter was cultivated in CSE minimal medium in the presence or absence of the inducer xylose. The transcriptomes of the two cultures (i.e. expressing RNase Y and depleted for RNase Y) were compared at a timepoint at which the reduced RNase Y amounts already affected the mRNA turnover whereas the growth rates of the two cultures were still almost identical.

2011-08-31 | E-GEOD-30430 | biostudies-arrayexpress

Microarray analysis of RNase I-deficient Escherichia coli versus wild-type BW25113

Project description:The present study investigated the role(s) of RNase I (encoded by the rna gene) in Escherichia coli by comparative gene expression analysis of an rna mutant and the isogenic wild-type E. coli strain BW25113. The transcriptomic analysis aims to provide mechanistic insight into aberrant phenotypes observed in the RNase I-deficient mutant.

2020-01-04 | E-MTAB-6095 | biostudies-arrayexpress

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