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Kinetically controlled competition between NusA and σ70 yields functionally diverse transcription elongation complexes

ABSTRACT: Kinetically controlled competition between NusA and σ70 yields functionally diverse transcription elongation complexes

PROVIDER: PRJNA435408 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6760333_1.fastq.gz	Fastqsanger.gz
	SRR6760333_2.fastq.gz	Fastqsanger.gz
	SRR6760334_1.fastq.gz	Fastqsanger.gz
	SRR6760334_2.fastq.gz	Fastqsanger.gz
	SRR6760335_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Kinetically controlled competition between NusA and σ70 yields functionally diverse transcription elongation complexes

Project description:In all organisms, the multi-subunit RNA polymerases (RNAPs) that synthesize messenger RNAs bind multiple accessory proteins to regulate transcript elongation rate, transcriptional pausing, and termination. However, the dynamics of regulatory protein association/dissociation and how different regulators influence one another’s function is unclear. We used single-molecule multi-wavelength fluorescence colocalization techniques to directly observe the dynamics of the elongation regulators NusA and σ70 with E. coli RNAP in vitro. Contrary to previous proposals, NusA was observed to repeatedly bind to and release from elongation complexes (ECs) during synthesis of a single RNA. However, elongation complexes that retained bound σ70 did not bind NusA and the EC-bound σ70 was largely retained even in the presence of physiological (µM) concentrations of competing elongation factors NusA and/or NusG. Factor occupancy of elongation complexes was non-equilibrium, with substantial amounts of σ70ECs even in the absence of free σ70, because composition was controlled by slow σ70 dissociation from σ70ECs. The experiments show that at steady state the same gene is transcribed by two distinct types of elongation complexes that are (ECs) or are not (σ70ECs) capable of binding NusA. Consistent with the known regulatory effects of NusA, the two types are observed to have different elongation rates, pausing dynamics, and efficiency of termination at an intrinsic terminator. During cellular transcription, these non-equilibrium populations of ECs are predicted to cause selective EC loss at intergenic transcriptional attenuators, traffic jams and altered pausing. This is an example of a potentially general “two-body” mechanism in which a functionally silent protein fine-tunes gene expression by modulating a second, functionally consequential regulator.

2020-08-20 | GSE110956 | GEO

E. coli MG1655 treated (G181D/R258C NusA) vs control (WT NusA) [II]

Project description:Transcription profiling of E. coli MG1655, representing the effect of G181D/R258C NusA in comparison to WT NusA

2016-03-28 | GSE77009 | GEO

E. coli MG1655 treated (G181D/R258C NusA) vs control (WT NusA) [I]

Project description:Transcription profiling of E. coli MG1655, representing the effect of G181D/R258C NusA in comparison to WT NusA

2016-03-28 | GSE77008 | GEO

NusA-dependent Transcription Termination Prevents Global Misregulation of Gene Expression

Project description:Canonical bacterial intrinsic terminators do not require additional factors for efficient transcription termination, although the general transcription elongation factor NusA was known to increase the termination efficiency slightly in vitro. We found that the effect of NusA varies widely among different terminators and identified a subclass of weak non-canonical terminators that largely depend on NusA for recognition by RNA polymerase. Using genome-wide 3’ end-mapping on an engineered Bacillus subtilis NusA depletion strain, we identified >2000 intrinsic terminators, hundreds of which are NusA-dependent. Our in vitro and in vivo characterization showed that terminators with weak RNA hairpins and distal U-tract interruptions tend to be NusA-dependent. Our observations indicate that the lethality associated with deletion of nusA is caused by global readthrough of NusA-dependent terminators, resulting in misregulation of physiologically important downstream genes. We also show that nusA expression is autoregulated by a transcription attenuation mechanism that is mediated by NusA-dependent termination.

2016-01-01 | GSE67058 | GEO

Transcriptome-wide effects of NusA on RNA polymerase pausing in Bacillus subtilis

Project description:In this work we conducted RNET-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this data we analysed the transcriptome-wide effects of NusA on RNA polymerase pausing and found that NusA has modest pause stimulating as well as suppressing effects throughout the genome.

2021-10-22 | GSE186285 | GEO

E. coli MG1655 treated (G181D/R258C NusA) vs control (WT NusA) [II]

Project description:Transcription profiling of E. coli MG1655, representing the effect of G181D/R258C NusA in comparison to WT NusA Agilent one-color experiment,Organism: Escherichia coli ,Agilent Custom Ecoli Gene Expression Microarray 2x400k designed by Genotypic Technology Private Limited. (AMADID:72220)

2016-03-28 | E-GEOD-77009 | biostudies-arrayexpress

E. coli MG1655 treated (G181D/R258C NusA) vs control (WT NusA) [I]

Project description:Transcription profiling of E. coli MG1655, representing the effect of G181D/R258C NusA in comparison to WT NusA Agilent one-color experiment,Organism: Escherichia coli ,Agilent Custom Escherichia coli Gene Expression Microarray 8x60K (AMADID: 48792) designed by Genotypic Technology Private Limited. , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

2016-03-28 | E-GEOD-77008 | biostudies-arrayexpress

NusA-dependent Transcription Termination Prevents Global Misregulation of Gene Expression

Project description:Canonical bacterial intrinsic terminators do not require additional factors for efficient transcription termination, although the general transcription elongation factor NusA was known to increase the termination efficiency slightly in vitro. We found that the effect of NusA varies widely among different terminators and identified a subclass of weak non-canonical terminators that largely depend on NusA for recognition by RNA polymerase. Using genome-wide 3â end-mapping on an engineered Bacillus subtilis NusA depletion strain, we identified >2000 intrinsic terminators, hundreds of which are NusA-dependent. Our in vitro and in vivo characterization showed that terminators with weak RNA hairpins and distal U-tract interruptions tend to be NusA-dependent. Our observations indicate that the lethality associated with deletion of nusA is caused by global readthrough of NusA-dependent terminators, resulting in misregulation of physiologically important downstream genes. We also show that nusA expression is autoregulated by a transcription attenuation mechanism that is mediated by NusA-dependent termination. 3' end-mapping and mRNA profiling of stationary phase B. subtilis NusA-depletion (PLBS802) strain in NusA expressing and depleted conditions, 6 replicates each.

2016-07-03 | E-GEOD-67058 | biostudies-arrayexpress

NusG is an intrinsic transcription termination factor that stimulates motility and cooperatively coordinates global gene expression with NusA

Project description:In this work we conducted Term-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this approach, we found that NusG is an intrinsic termination factor that works single and cooperatively with NusA.

2021-04-19 | GSE154522 | GEO

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (RNA-seq)

Project description:To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches, strand-specific RNA-seq and ChIP-seq, to survey the global transcriptome and monitor genome-wide dynamics of RNA polymerase (RNAP) and NusA. ChIP-seq revealed that RNAP and the antiterminator, NusA, occurred ubiquitously with the NusA profile mirroring RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the datasets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align.

2012-12-01 | GSE40846 | GEO

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