Effect of organic nitrogen on gene expression of clavulanic acid biosynthesis in Streptomyces clavuligerus F613-1
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ABSTRACT:
PROVIDER: PRJNA872036 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21160960_1.fastq.gz | Fastqsanger.gz | |||
| SRR21160960_2.fastq.gz | Fastqsanger.gz | |||
| SRR21160961_1.fastq.gz | Fastqsanger.gz | |||
| SRR21160961_2.fastq.gz | Fastqsanger.gz | |||
| SRR21160962_1.fastq.gz | Fastqsanger.gz |
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Project description:To investigate the function of organic nitrogen on clavulanic acid biosynthesis in Streptomyces clavuligerus, we established F613-1 strain cells cultured in MH fermentation medium and ML fermentation medium. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different medium at three time points.
2022-08-25 | GSE211765 | GEO
Project description:<p>Clavulanic acid (CA) is the preferred clinical drug for the treatment of infections by β-lactam antibiotic-resistant bacteria. CA is produced by <em>Streptomyces clavuligerus</em>, and although there have been many reports on the effects of carbon and nitrogen sources on CA production, the mechanisms involved remain unclear. In this study, we found that CA accumulation in <em>S. clavuligerus</em> F613-1 was increased significantly in MH medium, which is rich in organic nitrogen, compared with that in ML medium, which contains half the amount of organic nitrogen present in MH medium. Transcriptome analysis revealed that genes involved in CA biosynthesis, such as <em>ceas1</em>, <em>ceas2</em>, <em>bls1</em>, <em>bls2</em>, <em>cas2</em>, <em>pah2</em>, <em>gcaS</em>, and <em>cad</em>, and arginine biosynthesis, such as <em>argB</em>, <em>argC</em>, <em>argD</em>, <em>argG</em>, <em>argH</em>, <em>argJ</em>, and <em>argR</em>, were upregulated under rich organic nitrogen. Metabolome data revealed notable differences between cultures of F613-1 grown in MH and ML media with regard to levels of key intracellular metabolites, most of which are involved in arginine metabolic pathways, including arginine, glutamine, and glutamic acid. Additionally, supplementation of ML medium with arginine, glutamine, or glutamic acid resulted in increased CA production by <em>S. clavuligerus</em> F613-1. Our results indicate that rich organic nitrogen mainly affects CA biosynthesis by increasing the levels of amino acids associated with the arginine metabolic pathway and activating the expression of the CA biosynthetic gene cluster. These findings provide important insights for improving medium optimization and engineering of <em>S. clavuligerus</em> F613-1 for high-yield production of CA.</p>
2022-12-08 | MTBLS5744 | MetaboLights
Project description:Clavulanic acid is a clinically-important secondary metabolite used in treatment of infectious diseases. We aimed to decipher complex regulatory mechanisms acting in clavulanic acid biosynthesis through the analysis of transcriptome- and proteome-wide alterations in an industrial clavulanic acid overproducer Streptomyces clavuligerus, namely DEPA and its wild-type counterpart NRRL3585.
2022-11-02 | PXD032272 | Pride
Project description:Streptomyces clavuligerus F613-1 produces a clinically important β-lactamase inhibitor, clavulanic acid (CA). The biosynthesis pathway of CA has been basically elucidated, however, the global regulation of CA biosynthesis remains unclear. In order to further elucidate the regulatory mechanism of clavulanic acid synthesis, TCS RS07910/07915 which is next to the CA biosynthetic gene cluster was deleted in Streptomyces clavuligerus. F613-1. Deletion of RS07910/07915 results in decreased the production of CA, but the phenotype was not affected. Both the transcriptome and ChIP-seq data revealed that the TCS RS07910/07915 mainly regulate genes involved in primary metabolism (such as fatty acid degradation, glyceraldehyde 3-phosphate (G3P) metabolism, arginine biosynthesis) and CA biosynthesis. EMSA assays revealed that RS07915 could bind to the promoter fragments of argG, argC, oat1, oat2, ceaS1 and claR in vitro, indicating that RS07915 could direct regulate the biosynthesis genes of arginine and CA. This study indicated that RS07910/07915 is a pleiotropy regulatory TCS, RS07910/07915 could directly affect the biosynthesis of CA, and indirectly affect CA production through affecting primary metabolism of arginine and G3P (precursors of CA).
2018-08-30 | GSE119208 | GEO
Project description:To increase production of the important pharmaceutical compounds, both mutagenesis approaches and rational engineering have been extensively applied. Mutagenesis approaches are most popular in industry, but their effects have not yet been studied very well. Here, we used microarrays to compare the transcriptomes of the S. clavuligerus wild type (ATCC 27064) strain and the DS48802 clavulanic acid high-producer strain, which has been obtained by classical strain improvement (mutagenesis). Streptomyces clavuligerus strains were grown in shake flasks. RNA was extracted after 70h and hybridized to microarrays.
2010-11-10 | E-GEOD-24033 | biostudies-arrayexpress
Project description:To increase production of the important pharmaceutical compounds, both mutagenesis approaches and rational engineering have been extensively applied. Mutagenesis approaches are most popular in industry, but their effects have not yet been studied very well. Here, we used microarrays to compare the transcriptomes of the S. clavuligerus wild type (ATCC 27064) strain and the DS48802 clavulanic acid high-producer strain, which has been obtained by classical strain improvement (mutagenesis).
2010-11-10 | GSE24033 | GEO
Project description:Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
2018-11-30 | GSE110485 | GEO
Project description:Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using 15N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more by the higher organic matter addition, and the fraction of nitrogen loss attributed to anammox slightly reduced. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community as determined using a nirS microarray, indicating the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches.
2015-01-30 | GSE65430 | GEO
Project description:Welan gum is mainly produced by Sphingomonas sp. ATCC 31555 and has broad applications in industry such as that in cement production. Both carbon and nitrogen sources are essential for welan production. However, how nitrogen sources affect the metabolism and gene transcription of welan remains elusive. Here, we used next-generation sequencing RNA-seq to analyze the transcriptome of Sphingomonas sp. ATCC 31555 in the presence of inorganic or organic nitrogen sources. Enriched gene expression and pathway analysis suggest that organic nitrogen sources significantly enhanced the expression of genes in central metabolic pathways of Sphingomonas sp. ATCC 31555 and those critical for welan synthesis compared to that observed using inorganic nitrogen sources. The present study improves our understanding of the molecular mechanism underlying the use of nitrogen in welan synthesis in Sphingomonas sp., as well as provides an important transcriptome resource for Sphingomonas sp. in relation to nitrogen sources.
2016-03-25 | GSE79497 | GEO
Project description:Clavulanic acid (CA) is the preferred clinical drug for the treatment of infections by β-lactam antibiotic-resistant bacteria. CA is produced by Streptomyces clavuligerus, and although there have been many reports on the effects of carbon and nitrogen sources on CA production, the mechanisms involved remain unclear. In this study, we found that CA accumulation in S. clavuligerus F613-1 was increased significantly in MH medium, which is rich in organic nitrogen, compared with that in ML medium, which contains half the amount of organic nitrogen present in MH medium. Transcriptome analysis revealed that genes involved in CA biosynthesis, such as ceas1, ceas2, bls1, bls2, cas2, pah2, gcaS, and cad, and arginine biosynthesis, such as argB, argC, argD, argG, argH, argJ, and argR, were upregulated under rich organic nitrogen. Metabolome data revealed notable differences between cultures of F613-1 grown in MH and ML media with regard to levels of key intracellular metabolites, most of which are involved in arginine metabolic pathways, including arginine, glutamine, and glutamic acid. Additionally, supplementation of ML medium with arginine, glutamine, or glutamic acid resulted in increased CA production by S. clavuligerus F613-1. Our results indicate that rich organic nitrogen mainly affects CA biosynthesis by increasing the levels of amino acids associated with the arginine metabolic pathway and activating the expression of the CA biosynthetic gene cluster. These findings provide important insights for improving medium optimization and engineering of S. clavuligerus F613-1 for high-yield production of CA. IMPORTANCE The bacterium Streptomyces clavuligerus is used for the industrial production of the broad-spectrum β-lactamase inhibitor clavulanic acid (CA). However, much remains unknown about the factors which affect CA yields. We investigated the effects of different levels of organic nitrogen on CA production. Our analyses indicate that higher organic nitrogen levels were associated with increased CA yields and increased levels of arginine biosynthesis. Further analyses supported the relationship between arginine metabolism and CA production and demonstrated that increasing the levels of arginine or associated amino acids could boost CA yields. These findings suggest approaches for improving the production of this clinically important antibiotic.
| S-EPMC9927107 | biostudies-literature