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ABSTRACT: Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus

PROVIDER: PRJNA869557 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21075849.fastq.gz	Fastqsanger.gz
	SRR21075850.fastq.gz	Fastqsanger.gz

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An RNA sequencing data set revealing differentially expressed transcripts during ε-poly-L-lysine production in Streptomyces albulus.

Project description:Purpose: Streptomyces albulus is an industrial producer of ε-poly-L-lysine, an antimicrobial cationic homo poly-amino acid used practically as a natural food preservative. Here, we present RNA sequencing data set unveiling differentially expressed transcripts during ε-poly-L-lysine production in the most extensively studied poly-L-Lys producer, S. albulus NBRC14147. Methods: During the poly-L-Lys fermentation, cells grown for 8 hours and 35 hours were harvested as growth phase cells and production phase cells, respectively, and total RNA were extracted individually. A 100-bp paired-end mRNA sequencing was performed for each sample on the Illumina HiSeq 2500 system. Result: Using an optimized data analysis workflow, we were able to map more than 44 million sequence reads per sample to the reference genome (GenBank accession number ASM385166v1). Differential gene expression analysis was performed using the edgeR. The RNA-seq data revealed that a total of 2449 genes were considered to be differentially expressed during poly-L-Lys production using a fold change cutoff of log2 less than -1 and greater than 1 (equivalent to a ±2-fold change). Conclusion: Our data will serve as a primary source for investigating the regulatory mechanism which govern poly-L-Lys production in S. albulus NBRC14147.

2022-01-19 | GSE192684 | GEO

Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus

Project description:ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by S. albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering. Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18. Our results show that key genes in the glycolysis, glyoxylate, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. Furthermore, transcriptional and translational upregulation of genes involved in the tricarboxylic acid cycle, oxidative phosphorylation, and pentose phosphate pathway also increase the pools of available NADH, ATP, and NADPH. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure, thus further regulating the ε-PL biosynthesis. This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing a theoretical foundation development of advanced Streptomycetaceae microbial cell factories.

2023-07-20 | PXD036099 | Pride

Project description:Genomic and metabolomic analyses of Streptomyces albulus with enhanced epsilon-poly-L-lysine production through adaptive laboratory evolution

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An RNA sequencing data set revealing differentially expressed transcripts during ε-poly-L-lysine production in Streptomyces albulus.

Project description:An RNA sequencing data set revealing differentially expressed transcripts during ε-poly-L-lysine production in Streptomyces albulus.

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Project description:High-Level Poly-L-Lysine production in Streptomyces albulus by Multi-Omics-Guided Metabolic Engineering

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Transcriptional analysis of THP-1 cells stimulated by bacterial extracellular vesicles enriched by ultracentrifugation and an ε-poly- L-lysine-based method

Project description:We propose an isolation strategy based on a broad-spectrum antimicrobial epsilon-poly-L–lysine (ε-PL) to precipitate bacterial extracellular vesicles (BEVs) at a relatively low centrifugal speed (10,000 × g). Compared to the standard ultracentrifugation (UC) strategy, our method can enrich BEVs from large volumes of media inexpensively and rapidly. The precipitated BEVs can be recovered by adjusting pH and ionic strength of the media, followed by ultrafiltration step to remove ε-PL and achieve buffer exchange. To address whether BEVs isolated by these two methods lead to different host responses, we isolated Escherichia coli (E. coli) and Staphylococcus aureus BEVs from bacterial culture media using ultracentrifugation and our ε-poly- L-lysine-based method, respectively. Then we stimulated THP-1 cells with the isolated BEVs and the global transcript profiles were evaluated by the RNA-seq technique. Compared with the unstimulated THP-1 cells, BEV isolated by both methods could trigger a striking alteration in the gene expression pattern. Among the functions significantly enriched by these DEGs were immune response and leucocyte chemotaxis. The results indicated that the BEVs isolated by the ε-PL-based method also retained the in vitro biological activity as the commonly used ultracentrifugation.

2022-08-02 | GSE207009 | GEO

Project description:Enhancement of poly-L-lysine production by engineering sucrose metabolism pathway in Streptomyces albulus PD-1 using cane molasses

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RNA sequencing analysis of 5637 cells with D-xyl@epsilonPLCDs

Project description:We designed D-xylose-modified, epsilon-poly-L-lysine-based carbon dots (D-xyl@epsilonPLCDs) to effectively inhibit intracellular UPEC. D-xyl@εPLCDs effectively entered cells, reduced bacterial adhesion and promoted intracellular UPEC clearance. To investigate the regulation of immune responses in bladder epithelial 5637 cells after treatment with D-xyl@epsilonPLCDs, RNA sequencing analysis were performed.

2024-07-23 | GSE236507 | GEO

Time-course transcriptome analysis-guided identification of a four-component system, SbrH1-R that regulates milbemycin biosynthesis by influencing gene cluster expression, precursor supply, and antibiotic efflux

Project description:Streptomyces bingchenggensis is a soil bacterium that produces milbemycins, which have been applied widely as insecticides and anthelmintics in agricultural and veterinary field. To gain further insights into the regulatory mechanisms in Streptomyces bingchenggensis and mine useful targets for future metabolic engineering to improve milbemycin production, we have compared two strains（the parental strain and high-yielding strain）by comparative transcriptome analysis.This work provides beneficial targets and corresponding engineering methods to facilitate high-production of milbemycins and other polyketide pesticides.

2022-03-02 | GSE186852 | GEO

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