Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq, term-seq and tagRNA-seq of M. tuberculosis strains H37Rv and RhoDUC strains induced for Rho depletion at times 0H, 1.5H, 3H, 4.5H and 6H

ABSTRACT: Accurately controlled termination of transcription is critical for gene expression and adaptation to changing environments in bacteria. The aim of this study was to define transcription termination sites in Mycobacterium tuberculosis at nucleotide resolution. To this end, we used a combination of term-seq to identify termination of transcription and tagRNA-seq to identify transcription start sites and processed sites. This led us to identify a prevalence of Rho-dependent termination of transcription in the pathogen. We applied term-seq and WTSS RNA-seq on the RhoDUC strain derived from H37Rv, for which a depletion of Rho is inducible by addition of Anhydrous Tetracyclin, to identify Rho-responsive termination site and quantify readthrough.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mycobacterium tuberculosis H37Rv

SUBMITTER: Alexandre D'Halluin

PROVIDER: E-MTAB-11753 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

Rho and NusG suppress pervasive antisense transcription in Escherichia coli [RNA-seq].

Project description:Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its co-factor NusG is suppression of ubiquitous antisense transcription genome-wide. Rho binds C-rich unstructured nascent RNA (high C/G ratio) prior to its ATP-dependent dissociation of transcription complexes. NusG is required for efficient termination at minority subsets (~20%) of both antisense and sense Rho-dependent terminators with lower C/G ratio sequences. In contrast, a widely studied nusA deletion proposed to compromise Rho-dependent termination had no effect on antisense or sense Rho-dependent terminators in vivo. Global co-localization of the nucleoid-associated protein H-NS with Rho-dependent terminators and genetic interactions between hns and rho suggest that H-NS aids Rho in suppression of antisense transcription. The combined actions of Rho, NusG, and H-NS appear to be analogous to the Sen1-Nrd1-Nab3 and nucleosome systems that suppress antisense transcription in eukaryotes. RNA-seq experiments were performed on ribosome-depleted RNA from cells treated with 20 ug/ml bicyclomycin or untreated cells. The series contains 4 datasets.

2012-11-01 | E-GEOD-41939 | biostudies-arrayexpress

Characterization of two urea-utilizing pathways in coral reef ecosystems: implications for the significance of the urea cycle in facing global warming

Project description:Urea can serve as nitrogen source for coral holobionts and plays a cruscial role in coral calcification, although the degradation of urea by coral symbionts is not fully understood. In this study, we investigated the urea utilized pathway and the responses of the Symbiodiniaceae family to urea under high temperature conditions. Genome screening revealed that all Symbiodiniaceae species contain the urease (URE) and DUR2 subunit of urea amidolyase (UAD) system. However, only three speciesCladocopium goreaui, Cladopium c92, and Symbiodinium pilosum possess a complete UAD system, including both DUR1 and DUR2. Phylogentic analyses revealed that the UAD system in Symbiodiniaceae clusters more closely with symbiotic bacteria, indicating that horizontal gene transfer of UAD system has occured in coral symbionts. Physiology analysis showed that the symbiodiniacean species Cladocopium goreaui, which containing both URE and UAD, grew better under urea than ammonium conditions, as indicated by higher maximum specific growth rates. Furthermore, most genes of Symbiodiniaceae involved in urea utilization appeared to be stable under various conditions such as heat stress (HS), low light density, and nitrogen deficiency, wheras in ammonium and nitrate transporters were significantly regulated. These relatively stable molecular regulatory properties support sustained urea absorption by Symbiodiniaceae, as evidenced by an increase in δ15N2-urea absorption and the decreases in δ5N-NO3-, and δ15N-NH4+ from cultural environment to Symbiodiniaceae under HS conditions. Token together, this study reveals two distinct urea utilization systems in coral ecosystem and highlights the importance of the urea cycle in coral symbionts when facing fluctuating nitrogen environment in future warming ocean.

2024-09-27 | PXD056312 | Pride

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

Genome-wide analysis of transcriptional termination in E. coli

2008-05-16 | GSE10345 | GEO

Rho and NusG suppress pervasive antisense transcription in Escherichia coli [tiling array].

Project description:Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its co-factor NusG is suppression of ubiquitous antisense transcription genome-wide. Rho binds C-rich unstructured nascent RNA (high C/G ratio) prior to its ATP-dependent dissociation of transcription complexes. NusG is required for efficient termination at minority subsets (~20%) of both antisense and sense Rho-dependent terminators with lower C/G ratio sequences. In contrast, a widely studied nusA deletion proposed to compromise Rho-dependent termination had no effect on antisense or sense Rho-dependent terminators in vivo. Global co-localization of the nucleoid-associated protein H-NS with Rho-dependent terminators and genetic interactions between hns and rho suggest that H-NS aids Rho in suppression of antisense transcription. The combined actions of Rho, NusG, and H-NS appear to be analogous to the Sen1-Nrd1-Nab3 and nucleosome systems that suppress antisense transcription in eukaryotes. Tiling expression microarray experiments were performed in cells treated with 20 ug/ml bicyclomycin or cells deleted for nusG, or a partial deletion of nusA. Labeled cDNAs were hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 14 datasets.

2012-11-01 | E-GEOD-41938 | 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

2017-08-01 | GSE97559 | 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

The heme-responsive PrrH sRNA regulates Pseudomonas aeruginosa pyochelin gene expression

Project description:Pseudomonas aeruginosa is an opportunistic pathogen that requires iron for growth and virulence, yet this nutrient is sequestered by the innate immune system during infection. When iron is limiting, P. aeruginosa expresses the PrrF1 and PrrF2 small regulatory RNAs (sRNAs), which post-transcriptionally repress expression of non-essential iron-containing proteins thus sparing this nutrient for more critical processes.The genes for the PrrF1 and PrrF2 sRNAs are arranged in tandem on the chromosome, allowing for the transcription of a longer heme-responsive sRNA, termed PrrH. While the functions of PrrF1 and PrrF2 have been studied extensively, the role of PrrH in P. aeruginosa physiology and virulence is not well understood. In this study, we performed transcriptomic and proteomic studies to identify the PrrH regulon.

2023-08-11 | PXD040948 | Pride

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

2012-03-07 | GSE27303 | GEO