Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of the dose-dependent response of the ribosome-targeting antibiotic lincomycin on gene expression and its relationship to growth and secondary metabolism of S. coelicolor A3(2).

ABSTRACT: Lincomycin is a lincosamide antibiotic that forms cross-links within the peptidyl transferase loop region of the 23S rRNA of the 50S subunit of the bacterial ribosome, thereby inhibiting protein synthesis. We have previously reported that lincomycin at concentrations below the minimum inhibitory concentration potentiates the production of secondary metabolites in actinomycete strains. We aimed to elucidate the fundamental mechanisms underlying lincomycin induction of secondary metabolism in actinomycetes. Therefore, the dose-dependent response of lincomycin on gene expression of the model actinomycetes Streptomyces coelicolor A3(2) and possible relationships to secondary metabolism have been investigated.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Streptomyces coelicolor A3(2)

SUBMITTER: Hosaka Takeshi

PROVIDER: E-MTAB-6434 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The immediate effect of high-intensity green LED stimulation on the gene expression profile of S. coelicolor A3(2)

Project description:We investigated a novel, simple approach to induce the production of cryptic secondary metabolites in actinomycetes by stimulating the organism with high-intensity monochromatic green light (180 radiation unit). Streptomyces coelicolor A3(2) produces blue antibiotic actinorhodin (ACT) and red antibiotic undecylprodigiosin (RED). Using these two pigment antibiotics as indicators, we found that sporulation acceleration and regulation of the antibiotic production pathways can be induced by using high-intensity monochromatic green LEDs. Therefore, we investigated the immediate response of S. coelicolor A3(2) gene expression to the strong green LED stimulation.

2023-12-10 | E-MTAB-12876 | biostudies-arrayexpress

RNA-Sequencing of Streptomyces coelicolor A3(2) (M145) in timeseries

Project description:SYSTERACT: Systematic Rebuilding of Actinomycetes for Natural Product Formation For several decades antibiotics have saved millions of lives, but their overuse makes them less effective due to increase in bacterial resistance. Because of this major clinical and public health problem, there is an urgent need for new effective antimicrobials. The ERASysAPP project SYSTERACT aims to further develop, the model actinobacterium Streptomyces coelicolor into improved microbial cell factories to heterologously produce diverse bioactive compounds in amounts needed for structural and functional evaluation. Unprecedented systems biology understanding of S. coelicolor is being combined with morphology engineering and improved (de-)regulation and precursor supply to accelerate bioactive compound discovery efforts. By that means, we aim to generate a stepwise improved 'Superhost' for the production of antibiotics in which metabolic bottlenecks and regulatory restriction are greatly mitigated. The optimized strains will be tested concerning their applicability for an improved production of commercially relevant antibiotics and the expression of novel bioactive gene clusters identified in new actinomycete strains and environmental metagenomes. So far two strains, M145 and M1152, have been cultivated for time-resolved 'omics sampling, and a larger number of additional strains are on the list for similar experiments. High quality RNAseq-based transcriptome data have been generated and processed. M145 is the wildtype strain in S. coelicolor (as used in STREAM, see also GSE18489), 3 biol. replicas and M1152 lacks four major biosynthetic gene clusters, undecylprodigine (RED), calcium-dependent antibiotic (CDA), coelimycin (CPK) and actinorhodin (ACT). Contributors: A. Wentzel, W. Wohlleben, G. van Wezel, D van Dissel, O. Wolkenhauer, E. Kerkhoven, N. Spidsoe, K. Nieselt and the SYSTERACT consortium

2019-10-09 | GSE132487 | GEO

RNA-Sequenzing of Streptomyces coelicolor A3(2) (M1152) in timeseries

2019-10-09 | GSE132488 | GEO

Proteomics analysis of streptomyces sp. MBT76 demonstrates the production of qinichelins, new mixed catecholate-hydroxamate siderophores

Project description:Actinomycete genomes contain a plethora of orphan gene clusters encoding unknown secondary metabolites, and representing a huge unexploited pool of chemical diversity. The explosive increase in genome sequencing and the massive advance of bioinformatic tools have revolutionized the rationale for natural product discovery from actinomycetes. In this context, we applied a genome mining approach to discover a group of unique catecholate-hydroxamate siderophores termed as qinichelins from Streptomyces sp. MBT76. Quantitative proteomics statistically correlated a gene cluster of interest (qch) to its unknown chemotype (qinichelin), after which structural elucidation of isolated qinichelin was assisted by bioinformatics analysis and verified by MS2 and NMR experiments. Strikingly, intertwined functional crosstalk among four separately located gene clusters was implicated in the biosynthesis of qinichelins.

2018-10-24 | PXD006577 | Pride

Structure of Escherichia coli heat shock protein Hsp15 in complex with ribosomal 50S sununits bearing peptidyl-tRNA

Project description:In Escherichia coli, the heat shock protein 15 (Hsp15) is part of the cellular response to elevated temperature. Hsp15 interacts with peptidyl-tRNA-50S complexes that arise upon dissociation of translating 70S ribosomes, and is proposed to facilitate their rescue and recycling. A previous structure of E. coli Hsp15 in complex with peptidyl-tRNA-50S complex reported a binding site located at the central protuberance of the 50S subunit. By contrast, recent structures of RqcP, the Hsp15 homolog in Bacillus subtilis, in complex with peptidyl-tRNA-50S complexes have revealed a distinct site positioned between the anticodon-stem-loop (ASL) of the P-site tRNA and H69 of the 23S rRNA. Here we demonstrate that exposure of E. coli cells to heat shock leads to dissociation of 70S ribosomes and accumulation of 50S subunits, thus identifying a natural substrate for Hsp15 binding. Additionally, we have determined a cryo-EM reconstruction of the Hsp15-50S-peptidyl-tRNA complex isolated from heat shocked E. coli cells, revealing that Hsp15 binds to the 50S-peptidyl-tRNA complex analogously to its B. subtilis homolog RqcP. Collectively, our findings support a model where Hsp15 promotes access to the A-site for putative rescue factors to release the aberrant nascent polypeptide chain.

2022-11-15 | GSE216100 | GEO

RNA methylation-dependent RNA processing controls the speed of the circadian clock

Project description:To investigate the major components of the response to the methylation inhibitor 3-deazadenosine U2OS cells were plated in 20 cm dishes and grown until confluence. Cells were then treated with 100 microM deazaadenosine or vehicle (PBS) for 24 hours. Three replicate dishes for each treatment were analysed.

2013-11-07 | E-GEOD-48037 | biostudies-arrayexpress

HMGB1 signaling phosphorylates Ku70 and impairs DNA damage repair in Alzheimer’s disease pathology

Project description:DNA damage is increased in Alzheimer’s disease (AD), while the underlying mechanisms are unknown. Here, we employ comprehensive phosphoproteome analysis, and identify abnormal phosphorylation of 70 kDa subunit of Ku antigen (Ku70) at Ser77/78, which prevents Ku70-DNA interaction, in human AD postmortem brains. The abnormal phosphorylation inhibits accumulation of Ku70 to the foci of DNA double strand break (DSB), impairs DNA damage repair and eventually causes transcriptional repression-induced atypical cell death (TRIAD). Cells under TRIAD necrosis reveal senescence phenotypes. Extracellular high mobility group box 1 (HMGB1) protein, which is released from necrotic or hyper-activated neurons in AD, binds to toll-like receptor 4 (TLR4) of neighboring neurons, and activates protein kinase C alpha (PKCα) that executes Ku70 phosphorylation at Ser77/78. Administration of human anti-HMGB1 antibody to post-symptomatic AD model mice decreases neuronal DSBs, suppresses secondary TRIAD necrosis of neurons, prevents escalation of neurodegeneration, and ameliorates cognitive symptoms. TRIAD shares multiple features with senescence. These results newly unravel the HMGB1-Ku70 axis that accounts for the increase of neuronal DNA damage and secondary enhancement of TRIAD, the cell death phenotype of senescence, in AD.

2022-02-15 | PXD028089 | Pride

HuSE2,2Dvs3D

Project description:HCV proliferation is closely related to three-dimentional cellular condition. In case of blood-borne (bb) HCV culture in HuS-E2 cells, bbHCV was reproduced only from 3D-cultured cells in hollow fibers. Thus, in order to identify novel factors which support HCV proliferation under three-dimentional condition, we compared gene expression profile between 2D- and 3D-cultured HuS-E/2 cells with 3D-gene Human oligo chip 25k (Toray, Tokyo, Japan).

2013-12-10 | E-MTAB-1491 | biostudies-arrayexpress

R-proteins in modification deficient ribosomes - free 50S subunits

Project description:Ribosomal RNA modifications are introduced by specific enzymes during ribosome assembly in bacteria. Deletion of individual modification enzymes has a minor effect on bacterial growth, ribosome biogenesis, and translation, which has complicated the definition of the function of the enzymes and their products. We have constructed an E. coli strain lacking 10 genes encoding enzymes that modify 23S rRNA around the peptidyl-transferase center. This strain exhibits severely compromised growth and ribosome assembly, especially at lower temperatures. Ribosomal protein composition of the mature 50S ribosomes and free 50S subunits was analyzed by SILAC based qMS approach. We have found that absence of 23S rRNA modifications around PTC does not affect significantly r-protein content of incompletely assembled 50S or mature 50S ribosomes.

2024-03-15 | PXD047376 | Pride

R-proteins in modification deficient ribosomes - dissociated 50S subunits from 70S

2024-03-15 | PXD047588 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data