Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Streptomyces secondary metaboites - strain M1

ABSTRACT: In this study, we describe the isolation and identification of Streptomyces isolates collected from traditional medicinal plants’ rhizosphere during a campaign in Hamedan Province, Iran. Traditional medicinal plants represent a rich and unique source for the isolation of Streptomyces and new antimicrobial compounds. This strain was isolated from the rhizosphere of Helichrysum rubicundum

INSTRUMENT(S):

ORGANISM(S): Streptomyces Globisporus

SUBMITTER: Bart Devreese

LAB HEAD: Bart Devreese

PROVIDER: PXD042019 | Pride | 2024-01-04

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	220519_BDV_1M.mgf	Mgf
	220519_BDV_1M.wiff	Wiff
	220519_BDV_1M.wiff.scan	Wiff
	checksum.txt	Txt
	peptides_1_1_0.mzid.gz	Mzid

Items per page:

1 - 5 of 5

Similar Datasets

Streptomyces secondary metabolism

Project description:This project aims to discover novel bioactive compounds from Streptomyces isolated from the rhizosphere from wild medicinal plants from Hamedan province, Iran. Proteomics is used to assist in discovery and characterization of the compounds. Streptomyces isolates are grown on ISP-4 medium for three days, proteins were extracted and analysed by shotgun proteomics.

2024-01-04 | PXD041994 | Pride

Identification by ChIP-Seq of the binding sites of the extracytoplasmic function (ECF) sigma factor SigE in the genome of Streptomyces coelicolor A3(2) M600.

Project description:SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. This ChIP-Seq experiment was carried out to determine the binding sites of SigE under conditions of cell envelope stress induced by 10 ug / ml vancomycin for 30 minutes. A 3xFLAG tagged SigE was introduced in a SigE deletion strain and ChIP-Seq was carried out using M2 (Sigma Aldrich A2220) gel suspension. Non-immunoprecipitated (total) DNA preparations were used for background determination and the wild type M600 was used as the negative control.

2019-04-24 | E-MTAB-7827 | biostudies-arrayexpress

RNA-seq of various organs of Potentilla indica and Melastoma dodencadrum Lour.

Project description:Potentilla indica and Melastoma dodecandrum lour are medicinal herbs used in traditional Chinese medicine. We sampled the plants from Nanyang Technological University's herb garden for transcriptomics analysis.

2023-03-21 | E-MTAB-12682 | biostudies-arrayexpress

ChIP-Seq with anti-FLAG antibodies to determine binding of LexA-3xFLAG to DNA in Streptomyces venezuelae treated with Mitomycin C (MMC) overnight

Project description:LexA is a transcriptional repressor for genes requiring expression primarily during SOS response in response to stress such as that caused by DNA alkylating agent Mitomycin C (MMC). LexA undergoes self-cleavage under stress conditions thereby lifting the repression on genes whose expression is required for stress response. In our experiment LexA binding sites in the genome were determined in untreated and MMC treated (overnight, 14h) cultures using a LexA-3xFLAG strain and anti-FLAG monoclonal antibodies. Wild type Streptomyces venezuelae (unFLAGged LexA) cultures, with and without MMC treatment were used as negative controls.

2022-07-06 | E-MTAB-11603 | biostudies-arrayexpress

Transcriptome and translatome landscape of Streptomyces coelicolor M145

Project description:We have integrated nucleotide resolution genome-scale measurements of the transcriptome and translatome of the Streptomyces coelicolor A3(2), the model antibiotic-producing actinomycete. Our systematic study determined 3,473 transcription start sites, leading to discovery of a high proportion (~21%) of leaderless mRNAs and 230 non-coding RNAs; this enabled deduction of promoter architecture on a genome-scale. Ribosome profiling analysis revealed that the translation efficiency was negatively correlated for secondary metabolic genes. These results provide novel fundamental insights into translational regulation of secondary metabolism that enables rational synthetic biology approaches to awaken such âsilentâ secondary metabolic pathways. Profiles of primary transcripts, whole transcripts, and ribosome protected fragments (RPFs) of Streptomyces coelicolor were generated by deep sequencing using Illumina Miseq.

2016-05-28 | E-GEOD-69350 | biostudies-arrayexpress

Transcriptomic description of a classic model of carbon catabolic repression in Streptomyces coelicolor:Glk effect

Project description:The aim of this work was to use a high density microarray approach in Streptomyces coelicolor M145 and a glk substituted mutant (ScoZm)derived from it, to evaluate the paradigmatic model proposed for CCR in Streptomyces

2016-04-02 | E-MTAB-3602 | biostudies-arrayexpress

SvenBldMWhiIChIPSeq

Project description:To determine the influence of BldM and WhiI on the binding of each other to their respective binding sites in the genome of Streptomyces venezuelae, ChIP-Seq experiments were carried out using polyclonal antibodies against the wild type proteins as well as anti-FLAG antibodies against FLAG-tagged proteins. Null mutants of Streptomyces venezuelae lacking WhiI or BldM were used as controls. The wild tpe strain was used as control in experiments using the anti-FLAG antibodies.

2015-05-19 | E-MTAB-2698 | biostudies-arrayexpress

Vitis vinifera rhizosphere characterization: a metaproteome approach

Project description:Rhizosphere is a complex system of interactions between plant roots, bacteria, fungi and animals, where the release of plant root exudates stimulates bacterial density and diversity. However, the majority of the bacteria in soil results to be unculturable but active. The aim of the present work was to characterize the microbial community associated to the root of V. vinifera cv. Pinot Noir not only under a taxonomic perspective, but also under a functional point of view, using a metaproteome approach. Our results underlined the difference between the metagenomic and metaproteomic approach and the large potentiality of proteomics in describing the environmental bacterial community and its activity. In fact, by this approach, that allows to investigate the mechanisms occurring in the rhizosphere, we showed that bacteria belonging to Streptomyces, Bacillus and Pseudomonas genera are the most active in protein expression. In the rhizosphere, the identified genera were involved mainly in phosphorus and nitrogen soil metabolism.

2022-02-28 | PXD007670 | Pride

Influence of elevated atmospheric carbon dioxide on transcriptional responses of Bradyrhizobium japonicum in the soybean rhizosphere

Project description:Elevated atmospheric CO2 can influence the structure and function of rhizosphere microorganisms by altering root growth and the quality and quantity of compounds released into the rhizosphere via root exudation. In these studies we investigated the transcriptional responses of Bradyrhizobium japonicum cells growing in the rhizosphere of soybean plants exposed to elevated atmospheric CO2. Transciptomic expression profiles indicated that genes involved in carbon/nitrogen metabolism, and FixK2-associated genes, including those involved in nitrogen fixation, microanaerobic respiration, respiratory nitrite reductase, and heme biosynthesis, were significantly up-regulated under conditions of elevated CO2, relative to plants and bacteria grown under ambient CO2 growth conditions. The expression profile of genes involved in lipochitinoligosaccharide Nod factor biosynthesis and negative transcriptional regulators of nodulation genes, nolA and nodD2, were also influenced by plant growth under conditions of elevated CO2. Taken together, results of these studies indicate that growth of soybeans under conditions of elevated atmospheric CO2 influences gene expressions in B. japonicum in the soybean rhizosphere, resulting in changes to carbon/nitrogen metabolism, respiration, and nodulation efficiency. Bradyrhizobium japonicum strains were grown in the soybean rhizosphere under two different CO2 concentrations. Transcriptional profiling of B. japonicum was compared between cells grown under elevated CO2 and ambient conditions. Four biological replicates of each treatment were prepared, and four microarray slides were used for each strain.

2010-07-28 | E-GEOD-23296 | biostudies-arrayexpress

GeoChip data of soil microbial communities in the maize rhizosphere and bulk soils

Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method. Triplicate samples were taken for both rhizosphere and bulk soil, in which each individual sample was a pool of four plants or soil cores. To determine the abundance of functional genes in the rhizosphere and bulk soils, GeoChip 3.0 was used.

2014-09-12 | E-GEOD-61338 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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