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An antibiotic-sensing leader peptide regulates translation and premature Rho-dependent transcription termination of the topAI gene in Escherichia coli

ABSTRACT: An antibiotic-sensing leader peptide regulates translation and premature Rho-dependent transcription termination of the topAI gene in Escherichia coli

PROVIDER: PRJEB34533 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3537780_1.fastq.gz	Fastqsanger.gz
	ERR3537780_2.fastq.gz	Fastqsanger.gz
	ERR3537783_1.fastq.gz	Fastqsanger.gz
	ERR3537783_2.fastq.gz	Fastqsanger.gz
	ERR3537784_1.fastq.gz	Fastqsanger.gz

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Rho stimulates both Rho-dependent and intrinsic termination in Bacillus subtilis

Project description:In this work we conducted Term-seq on Wild Type B. subtilis, and strains compromosing all logical mutations in all combinations of the genes that encode for NusA, NusG, and Rho, where we developed the first transcription termination atlas. We used this atlas to find that Rho can stimulate intrinsic termination in B. subtilis and we recapitulated this finding in vitro to dissect the mechanism.

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An antibiotic-sensing leader peptide regulates translation and premature Rho-dependent transcription termination of the topAI gene in Escherichia coli

Project description:The SHAPE-Seq experiment was used to determine accessible nucleotides in the 5' UTR of the topAI gene in the presence and absence of 0.2 ug/ml of tetracycline.

2019-10-03 | E-MTAB-8365 | biostudies-arrayexpress

Rho dependent transcription termination is a dominant mechanism of transcription termination in Mycobacterium tuberculosis

Project description:Rho dependent transcription termination is a dominant mechanism of transcription termination in Mycobacterium tuberculosis

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Rho stimulates both Rho-dependent and intrinsic termination in Bacillus subtilis

Project description:Rho stimulates both Rho-dependent and intrinsic termination in Bacillus subtilis

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Transcriptome analysis of a Bacillus subtilis mutant defective in the transcription termination factor Rho.

Project description:This analysis is part of the study GSE27219, The condition-dependent transcriptome of Bacillus subtilis 168. In this study, 120 transcription units where identified for which transcription did not terminate at any specific site, leading to mRNA extension over long distances with slowly decreasing signal intensity. In most cases, lack of termination and read-through generated antisense transcripts. These findings together with the lack of intrinsic terminators suggested that transcription termination of the 120 transcription units could be mediated by the transcription termination factor Rho. In order to investigate the impact of Rho-mediated termination, tiling array hybridizations using RNA samples of a B. subtilis rho-null mutant and its parental strain were performed. B. subtilis 1012 wild-type and rho-mutant cells were grown in LB medium. Samples for tiling array analysis were taken during exponential growth phase. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

2012-03-07 | E-GEOD-27303 | biostudies-arrayexpress

Rho directs widespread termination of intragenic and stable RNA transcription

Project description:The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found ~200 Rho-terminated loci that were divided evenly into two classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a novel set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a novel role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation. Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (Beta or Beta' subunit) in cells treated with 20ug/ml bicyclomycin or untreated cells. Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 4 datasets.

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Rho directs widespread termination of intragenic and stable RNA transcription

2009-06-23 | GSE16562 | GEO

Transcriptome analysis of a Bacillus subtilis mutant defective in the transcription termination factor Rho.

2012-03-07 | GSE27303 | GEO

Transcription profiling of E. coli inhibited for Rho activity to assess Rho function

Project description:Transcription termination factor Rho is essential in enterobacteria. We inhibited Rho activity with bicyclomycin and used microarray experiments to assess Rho function on a genome-wide scale. Rho is a global regulator of gene expression that matches E. coli transcription to translational needs. Remarkably, genes that are most repressed by Rho are prophages and other horizontally-acquired portions of the genome. Elimination of these foreign DNA elements increases resistance to bicyclomycin. Although rho remains essential, such reduced-genome bacteria no longer require Rho cofactors NusA and NusG. Thus, Rho termination, supported by NusA and NusG, is required to suppress the toxic activity of foreign DNA. Global regulation of transcription termination by Rho, NusA, and NusG. Experiment Overall Design: Two sets of experiments are presented. First, treatment of E. coli with Rho inhibitor bicyclomycin was performed in strains MG1655 and O157:H7 EDL933 for twenty minutes at concentrations of 10, 25, or 100 micrograms/milliliter. In the second set of experiments the reduced-genome strain MDS42 was treated with bicyclomycin as well as having deletions of the genes nusA and nusG. Total RNA was extracted and hybridized to the Affymetrix E. coli Genome 2.0 array, which contains complete genome coverage of four strains of E. coli.

2008-06-20 | E-GEOD-10345 | biostudies-arrayexpress

A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [sRNA-seq]

Project description:Co-transcriptional RNA processing and surveillance factors mediate heterochromatin formation in fission yeast. In addition to RNAi, RNA elimination machinery including MTREC (Mtl1-Red1 core) and the exosome are involved in facultative heterochromatin assembly, however, the exact mechanisms remain unclear. Here we show that RNA elimination factors cooperate with the conserved exoribonuclease Dhp1/Rat1/Xrn2, which couples pre-mRNA 3â-end processing to transcription termination, to promote premature termination and facultative heterochromatin formation at meiotic genes. Dhp1 also affects termination of transcripts at genes that are targets of RNAi-mediated heterochromatin assembly. Moreover, Dhp1 facilitates constitutive heterochromatin formation and silencing at centromeric and mating-type loci. Remarkably, we find that Dhp1 interacts with the Clr4/Suv39h methyltransferase complex and acts directly to nucleate heterochromatin. Our results uncover a novel role for 3â-end processing and termination machinery in gene silencing through premature termination and suggest that non-canonical termination by Dhp1 and RNA elimination factors is linked to heterochromatin assembly. These findings have important implications for understanding mechanisms of gene silencing in higher eukaryotes. Sequencing and analysis of small RNA in two S. pombe mutants

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