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Transcriptome analysis of wild type and erythromycin-producing strain of S. erythraea

ABSTRACT: Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. We used transcriptomic approach to compare whole genome expression in erythromycin high-producing strain, compared to the wild type S. erythraea strain in four stages of fermentation. 2 strains (3 individual fermentations each), 4 time points --> 24 samples (2 exluded from anaysis, 22 remaining); one color design

ORGANISM(S): Saccharopolyspora erythraea

SUBMITTER: Spela Baebler

PROVIDER: E-GEOD-65007 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea.

Karničar Katarina K Drobnak Igor I Petek Marko M Magdevska Vasilka V Horvat Jaka J Vidmar Robert R Baebler Špela Š Rotter Ana A Jamnik Polona P Fujs Štefan Š Turk Boris B Fonovič Marko M Gruden Kristina K Kosec Gregor G Petković Hrvoje H

Microbial cell factories 20160603

<h4>Background</h4>Omics approaches have significantly increased our understanding of biological systems. However, they have had limited success in explaining the dramatically increased productivity of commercially important natural products by industrial high-producing strains, such as the erythromycin-producing actinomycete Saccharopolyspora erythraea. Further yield increase is of great importance but requires a better understanding of the underlying physiological processes.<h4>Results</h4>To ...[more]

PMID: 27255285

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Transcriptome analysis of wild type and erythromycin-producing strain of S. erythraea

Project description:Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. We used transcriptomic approach to compare whole genome expression in erythromycin high-producing strain, compared to the wild type S. erythraea strain in four stages of fermentation.

2016-06-22 | GSE65007 | GEO

Phenotype and expression profile of S. erythraea rifampicin-resistant (rif) mutants affected in erythromycin production

Project description:In this study we have used the rifampicin selection as a tool to genetically improve the erythromycin producer Saccharopolyspora erythraea. Two rifampicin-resistant (rif) mutants, rif1 and rif6, have been characterized in more detail. With respect to the parental strain NRRL2338, rif1 (harboring the missense S444F) exhibited higher respiratory performance and final erythromycin yields; in contrast, rif6 (harboring the missense Q426R) was slow-growing, developmental-defective and severely impaired in erythromycin production. The results of genome-wide analysis of expression profiles using DNA micro-arrays demonstrated that these mutations deeply changed the transcriptional profile of S. erythraea with marked regional distribution. Keywords: mutants versus wild type comparison in a time course experiment

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Physiological responses of Saccharopolyspora erythraea towards perturbation of intracellular ATP

Project description:Saccharopolyspora erythraea is used for industrial-scale production of erythromycin. To explore the physiological role of co-factors in regulation of primary and secondary metabolism of S. erythraea, we initially overexpressed the endogenous F1-ATPase in an erythromycin high-producing strain, E3. The engineered strain is named EA. The F1-ATPase expression resulted in a lower [ATP]/[ADP] ratio, which was accompanied by a dramatic increased production of a reddish pigment and a decreased erythromycin production. Transcriptional analysis revealed that the intracellular [ATP]/[ADP] ratio appeared to exert a global regulation on the metabolism of S.erythraea, and the lower [ATP]/[ADP] ratio induced physiological changes to restore the energy balance, mainly via pathways that tend to produce ATP or NADH. The results also indicated a state of redox stress in the engineered strain, which was correlated to the alteration of electron transport at the branch of the terminal oxidases.

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Saccharopolyspora erythraea LC-MSMS

Project description:Lysine acetylation is a dynamic, reversible post-translational modification that is known to play an important role in regulating the activity of many key enzymes in bacteria. Acetylproteome studies have been performed on some bacteria. However, until now there have been no data on the Actinomycetes, which are the major producers of therapeutic antibiotics. In this study, we investigated the first acetylproteome of the erythromycin-producing Actinomycete Saccharopolyspora erythraea using a high-resolution mass spectrometry-based proteomics approach. Using immune-affinity isolation of acetyl-peptides with an anti-acetyllysine antibody followed by nano-UPLC/MS/MS analysis, we identified 664 unique lysine acetylated sites on 363 proteins.

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Effect of artificial control system (hQSCS) on native transcriptome of S. erythraea during erythromycin fermentation

Project description:Reconstructing an artificial control system orthogonal to the native regulatory network of Saccharopolyspora erythraea is critical for circumventing the constraints imposed by its complex endogenous regulation. Here, we present a transcriptional profiling dataset of S. erythraea strain harboring the heterologous QS control system (hQSCS) during erythromycin fermentation. This dataset was generated to characterize the transcriptional response of host cells upon activation of the heterologous hQSCS. Specifically, RNA sequencing was performed on strain without hQSCS (control) and hQSCS engineered strain (treatment), both cultured in TSB medium for 72 h. Differential expression analysis of this dataset will help determine whether hQSCS exerts regulatory crosstalk with the native transcriptome of S. erythraea, which is essential for verifying the orthogonality of hQSCS. Collectively, this transcriptional dataset provides a valuable resource for investigating the orthogonality of hQSCS in S. erythraea and offers insights into the development of orthogonal control systems for other rare actinomycetes.

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Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea

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Saccharopolyspora erythraea

Project description:Transcriptome analysis of wild type and erythromycin-producing strain of S. erythraea

| PRJNA272711 | ENA

Physiological responses of Saccharopolyspora erythraea towards perturbation of intracellular NADH/NAD+

Project description:Knowledge about effects of cofactor perturbation on cellular metabolism is scarce with respect to Saccharopolyspora erythraea. The water-forming NADH oxidase (NOX) from Streptococcus pneumonia was expressed in S.erythraea E3, an important industrial strain for erythromycin production, at three different levels to investigate effects of intracellular redox status on secondary metabolism. NOX expression reduced the intracellular [NADH]/[NAD+] ratios significantly, although with a strong constitutive promoter NOX function was limited due to the shortage of oxygen. We demonstrated the negative correlation between [NADH]/[NAD+] ratios and biosynthesis of erythromycin in S.erythraea, but a positive correlation between the redox ratios and pigment production as well. We furthermore completed next-generation RNA sequencing of E3 and two NOX-expression strains. The transcription results showed that transfer processes of carbohydrates, DNA and chemical groups were altered resulting in metabolic shifts to supply more NADH for NOX fully functioning. Additionally, redox status affected transcription of several genes by allosteric effects on their transcription initiation. Specifically, transcriptional analysis along with enzymatic assay suggested that redox status influenced biosynthesis of erythromycin indirectly by allosteric effects on biosynthesis of the secondary messenger, c-di-GMP. The present work provides a basis for future cofactor manipulation in S.erythraea for further improvement of erythromycin production.

2020-08-04 | GSE144067 | GEO

Saccharopolyspora erythraea RNA-seq

Project description:We report the high-throughput profiling of saccharopolyspora erythraea including a industrial strain HL3168 E3 and a wild-type strain NRRL23338. The aim was to evaluate the difference in expression of sRNA predicted in silico related to secondary metabolites in Saccharopolyspora erythraea.

2013-07-16 | GSE48887 | GEO

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