Detoxins S1, N1, N2, N3, P1, P2, P3 source strain raw UHPLC-MS data and representative MS2
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Streptomyces Sp. Nrrl B-1347 Streptomyces Spectabilis Nrrl 2792 Amycolatopsis Jujuensis Nrrl B-24427 Streptomyces Sp. S-325
SUBMITTER: 
Neil L Kelleher
PROVIDER: MSV000083648 | MassIVE | Mon Apr 01 10:19:00 BST 2019
REPOSITORIES: MassIVE
Similar Datasets
Project description:This study aimed to investigate the variations in the protein composition of Streptomyces sp. PU10 when cultivated with either Impranil (polyestere-polyurethane) or glucose as the carbon source. We analyzed both the intracellular and extracellular protein fractions to gain insights into the intricate processes involving PU degradation, intermediate metabolic pathways in PU degradation, and the connection between primary and secondary metabolism within Streptomyces sp. PU10.
2024-03-29 | PXD047534 | Pride
Project description:Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions: The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high.
2011-07-15 | GSE30680 | GEO
Project description:Investigation of whole genome gene expression level changes in Streptomyces sp. SirexAA-E (ActE) when grown on different carbon sources. The results of this study demonstrate that ActE upregulates a small number of genes specific for the utilization of the avaliable carbon source. Cellulolytic Streptomyces sp. SirexAA-E (ActE), isolated from the pinewood-boring wasp Sirex noctilio, has a genome enriched for biomass utilization. The secreted proteomes obtained from growth on pure polysaccharides catalyzed hydrolysis of cellulose, mannan, and xylan with specific activities comparable to Spezyme CP, a commercial cellulase preparation. During reaction of an ActE secretome with cellulose, reducing sugar release was markedly stimulated in the presence of O2. ActE also expresses and secretes an expanded repertoire of enzymes during growth on natural and pre-treated biomass. These results indicate a new microbial contribution to biomass utilization that is widely distributed in natural environments by insects Streptomyces sp. ActE was grown in minimal medium supplimented with 0.5% carbon source (glucose, sigmacell-20, xylan, chitin, cellobiose, or AFEX). Cells were grown for 7 days and total RNA was extracted from the cell pellet. At least 3 biological replicates were performed for each carbon source (glucose, 3; sigmacell, 3; xylan, 5; chitin, 3; cellobiose 3; AFEX 3). Each biological replicate contained 3 technical replicates. The complete dataset were RMA Background Corrected, quantile normalized, the RMA algorithm was utilized by DNAStar ArrayStar.
2013-12-31 | E-GEOD-31748 | biostudies-arrayexpress
Project description:Streptomyces sp. M7 has demonstrated ability to remove lindane from culture media and soils. In this study, we used MS-based label-free quantitative proteomic to understand lindane degradation and its metabolic context in Streptomyces sp. M7. We identified the proteins involved in the up-stream degradation pathway. Our results demonstrated that mineralization of lindane is feasible since proteins from an unusual down-stream degradation pathway were also identified. Degradative steps were supported by an active catabolism that supplied energy and reducing equivalents in the form of NADPH. This is the first study in which degradation steps of an organochlorine compound and metabolic context are elucidate in a biotechnological genus as Streptomyces. These results serve as basement to study other degradative actinobacteria and to improve the degradation processes of Streptomyces sp. M7.
2018-08-10 | PXD010607 | Pride
Project description:Investigation of whole genome gene expression level changes in Streptomyces sp. SirexAA-E (ActE) when grown on different carbon sources. The results of this study demonstrate that ActE upregulates a small number of genes specific for the utilization of the avaliable carbon source. Cellulolytic Streptomyces sp. SirexAA-E (ActE), isolated from the pinewood-boring wasp Sirex noctilio, has a genome enriched for biomass utilization. The secreted proteomes obtained from growth on pure polysaccharides catalyzed hydrolysis of cellulose, mannan, and xylan with specific activities comparable to Spezyme CP, a commercial cellulase preparation. During reaction of an ActE secretome with cellulose, reducing sugar release was markedly stimulated in the presence of O2. ActE also expresses and secretes an expanded repertoire of enzymes during growth on natural and pre-treated biomass. These results indicate a new microbial contribution to biomass utilization that is widely distributed in natural environments by insects
2013-12-31 | GSE31748 | GEO
Project description: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
2024-01-04 | PXD042019 | Pride
Project description:The objective of this study was to assess whether Methylocystis sp. strain SC2, as a representative for Methylocystis spp., can utilize hydrogen to optimize the biomass yield by mixed utilization of CH4 and H2, rather than CH4 as the sole source of energy. Thus, we aimed to show that, in the presence of H2, CH4 will primarily be used for synthesis of cell carbon and increased biomass/protein yield. In particular, we intended to explore those CH4/O2 ratios, which maximize the effect of hydrogen addition on the biomass yield and proteome reconstruction of strain SC2. To achieve our goals, we combined hydrogen-based growth experiments with our recently optimized proteomics workflow.
2020-06-03 | PXD015700 | Pride
Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RybB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RybB in a rne131 ΔrybB strain. RybB (without MS2) was used as control
2015-04-16 | E-GEOD-66518 | biostudies-arrayexpress
Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RyhB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RyhB in a rne131 ?ryhB strain. RyhB (without MS2) was used as control
2015-04-16 | E-GEOD-66519 | biostudies-arrayexpress
Project description:Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions: The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high. Detection of gene expression variance among Frankia HfpCci3 (Cci3) cells grown in ammonium chloride for three days, five days and HfpCci3 cells grown in nitrogen fixing conditions for three days using mRNA-seq
2011-07-15 | E-GEOD-30680 | biostudies-arrayexpress