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The transcription dynamics in Actinoplanes sp. SE50/110 during growth.

ABSTRACT: The transcription dynamics in Actinoplanes sp. SE50/110 during growth.

PROVIDER: PRJEB37141 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3981090.fastq.gz	Fastqsanger.gz
	ERR3981100.fastq.gz	Fastqsanger.gz
	ERR3981110.fastq.gz	Fastqsanger.gz
	ERR3981091.fastq.gz	Fastqsanger.gz
	ERR3981101.fastq.gz	Fastqsanger.gz

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The transcription dynamics in Actinoplanes sp. SE50/110 during growth.

Project description:Actinoplanes sp. SE50/110 was grown in three biological replicates in fermenter cultivation in maltose minimal medium. The transcriptomic changes during growth were monitored by sampling every 24 h. RNA-seq of all 7 replicates and a pooled RNA sample of all time points of each fermenter was performed in Paired-End mode (2x 70 nt) using Illumina HiSeq. Mapping to the reference genome (GenBank: LT825010.1) was perfromed using bowtie2 Version 2.3.2.

2020-04-01 | E-MTAB-8857 | biostudies-arrayexpress

Proteome Analysis of Actinoplanes sp. SE50/110

Project description:The acarviose metabolite acarbose is an a glucosidase inhibitor produced by Actinoplanes sp. SE50/110. It is medically important because it is used in the treatment of type 2 diabetes. In this work a comprehensive proteome analysis of Actinoplanes sp. SE50/110 was carried out. The associated txt and RAW files were used for two different analyses and publications. While one study focused on a comparative analysis of Actinoplanes sp. SE50/110 to elucidate differences in the proteome cultures that were grown with either maltose or glucose, the other study applied spectral counting and analyzed only the maltose-grown cultures to determine the major proteins and their location in the cell. The txt files for the comparative data are labeled as "heavy_light" and of the spectral counting data as "light". Both datasets were derived from the same RAW files.

2015-10-21 | PXD001497 | Pride

Actinoplanes sp. SE50/110

Project description:Actinoplanes sp. SE50/110 Genome sequencing

| PRJNA76835 | ENA

Comparative microarrays of Actinoplanes sp. SE50/110 ΔacrA with the Actinoplanes sp. SE50/110 wildtype

Project description:In order to characterize the transcriptional regulator AcrA, comparative genome wide transcriptome analyses were conducted. Therefore, the wild type Actinoplanes sp. SE50/110 and the mutant ΔacrA were each cultivated in triplicates in minimal medium supplemented with maltose or glucose as single carbon source. RNA samples from the biological replicates were taken from the middle of the growth phase of both strains in each maltose and glucose minimal medium, respectively. RNA was isolated and the three replicates were combined for each strain and condition. For each cultivation condition, the data from two arrays (dye swap) were combined to make statistically reliable conclusions.

2017-06-30 | E-MTAB-5459 | biostudies-arrayexpress

Comparative microarrays of Actinoplanes sp. SE50/110 ΔmalT with the Actinoplanes sp. SE50/110 wildtype

Project description:In order to characterize the transcriptional regulator MalT, comparative genome wide transcriptome analyses were conducted. Therefore, the wild type Actinoplanes sp. SE50/110 and the mutant ΔmalT were each cultivated in triplicates in minimal medium supplemented with maltose or glucose as single carbon source. RNA samples from the biological replicates were taken from the middle of the growth phase of both strains in each maltose and glucose minimal medium, respectively. RNA was isolated and the three replicates were combined for each strain and condition. For each cultivation condition, the data from two arrays (dye swap) were combined to make statistically reliable conclusions.

2020-04-01 | E-MTAB-8815 | biostudies-arrayexpress

The expression of the acarbose biosynthetic gene cluster of Actinoplanes sp. SE50/110 is dependent on the growth phase

Project description:Actinoplanes sp. SE50/110 produces the diabetes type II drug acarbose only during the growth phase and not in the stationary phase. This correlation between the course of the cell growth and the biosynthesis could be due to a decreasing expression of the acarbose biosynthesis genes until the stationary phase. Therefore, a genome wide transcriptome and proteome analysis in a high temporal resolution is well suited to study the acarbose biosynthesis and the transcriptional regulation thereof. In this study, RNA-seq data and state-of-the-art proteomic data from seven time points of controlled bioreactor cultivations were used to analyze expression dynamics during growth of Actinoplanes sp. SE50/110. A hierarchical cluster analysis revealed co-regulated genes, which display the same transcription dynamics over the cultivation time. Typical indications for a metabolic switch from primary metabolism to secondary metabolism could be detected when the cells entered the stationary phase of growth. In this transition phase, a decreasing transcript abundance for all acarbose biosynthetic genes was observed, with the strongest decrease for the monocistronically transcribed genes acbA, acbB, acbD and acbE. The transcription of these genes shows the same pattern as the specific product formation rate of acarbose, indicating a correlation. However, the proteome dynamics does not follow the respective transcription for all genes. This suggests different protein stabilities of the Acb proteins, which in turn could be an indication for bottlenecks in the acarbose biosynthesis.

2021-09-09 | PXD017973 | Pride

RNA-seq of coding RNA of Actinoplanes sp. SE50/110 to analyze gene function of alternative sigma factor gene ACSP50_0507

Project description:Cultivation in maltose minimal media and sampling at different time point (t2 = 96h; t3=118h; t4 = 142h; t5 = 166h) of Actinoplanes sp. SE50/110 empty vector control and Actinoplanes sp. SE50/110 ACSP50_0507 overxepression mutant. RNAseq material and methods

2024-07-22 | E-MTAB-13644 | biostudies-arrayexpress

Whole track RNAseq of the deletion mutant delta cgt in Actinoplanes sp. SE50/110 during growth phase and during transition into stationary phase

Project description:Actinoplanes sp. SE50/110 (ATCC 31044) is the wild type of industrial producer strains of acarbose. Acarbose is used since the early 1990s as an inhibitor of intestinal human alpha-glucosidases in the medical treatment of type II diabetes mellitus. The small secreted protein Cgt, which consists of a single carbohydrate-binding module (CBM) 20-domain, was found to be highly expressed in Actinoplanes sp. SE50/110 in previous studies, but neither its function nor a possible role in acarbose formation was explored, yet. Due to this and its high abundance in the extracellular proteome of Actinoplanes, a functional role within the sugar metabolism or in the environmental stress protection was assumed. However, the gene deletion mutant ∆cgt, constructed by CRISPR/Cas9 technology, displayed no apparent phenotype in screening experiments testing for pH and osmolarity stress, limited carbon source starch as well as excess of seven different sugars in liquid culture and further 97 carbon sources in the Omnilog Phenotypic Microarray system of Biolog. Therefore, a protective function as a surface protein or a function within the retainment and the utilization of carbon sources could not be experimentally validated. Remarkably, enhanced production of acarbose was determined yielding into 8-16 % higher product titers when grown in maltose-containing medium. Here the whole track RNAseq data of delta cgt and the wild type of Actinoplanes sp. SE50/110 during growth phase and during transition into stationary phase are provided, when grown in maltose minimal medium.

2020-09-01 | E-MTAB-8432 | biostudies-arrayexpress

Sequencing of different Actinoplanes sp. SE50/110 mutants

Project description:Sequencing of different Actinoplanes sp. SE50/110 mutants

| PRJEB12637 | ENA

Improved genome sequence of Actinoplanes sp. SE50/110

Project description:Improved genome sequence of Actinoplanes sp. SE50/110

| PRJEB15656 | ENA