Multi-omics analysis of mutagenized S. rimosus reveals synergistic changes that drive oxytetracycline production towards industrial efficiency and opens a new route to heterologous polyketides
Ontology highlight
ABSTRACT:
ORGANISM(S): Streptomyces rimosus subsp. rimosus
PROVIDER: GSE232318 | GEO | 2023/05/16
REPOSITORIES: GEO
Similar Datasets
Project description:The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.
2024-01-26 | PXD042182 | Pride
Project description:Abstract: Transcript levels in production cultures of wildtype and classically improved strains of the actinomycete bacteria Saccharopolyspora erythraea and Streptomyces fradiae were monitored using microarrays of the sequenced actinomycete S. coelicolor. Sac. erythraea and S. fradiae synthesize the polyketide antibiotics erythromycin and tylosin, respectively, and the classically improved strains contain unknown overproduction mutations. The Sac. erythraea overproducer was found to express the entire 56-kb erythromycin gene cluster several days longer than the wildtype strain. In contrast, the S. fradiae wildtype and overproducer strains expressed the 85-kb tylosin biosynthetic gene cluster similarly, while they expressed several tens of other S. fradiae genes and S. coelicolor homologs differently, including the acyl-CoA dehydrogenase gene aco and the S. coelicolor isobutyryl-CoA mutase homolog icmA. These observations indicated that overproduction mechanisms in classically improved strains can affect both the timing and rate of antibiotic synthesis, and alter the regulation of antibiotic biosynthetic enzymes and enzymes involved in precursor metabolism. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4395 | GEO
Project description:Abstract: Transcript levels in production cultures of wildtype and classically improved strains of the actinomycete bacteria Saccharopolyspora erythraea and Streptomyces fradiae were monitored using microarrays of the sequenced actinomycete S. coelicolor. Sac. erythraea and S. fradiae synthesize the polyketide antibiotics erythromycin and tylosin, respectively, and the classically improved strains contain unknown overproduction mutations. The Sac. erythraea overproducer was found to express the entire 56-kb erythromycin gene cluster several days longer than the wildtype strain. In contrast, the S. fradiae wildtype and overproducer strains expressed the 85-kb tylosin biosynthetic gene cluster similarly, while they expressed several tens of other S. fradiae genes and S. coelicolor homologs differently, including the acyl-CoA dehydrogenase gene aco and the S. coelicolor isobutyryl-CoA mutase homolog icmA. These observations indicated that overproduction mechanisms in classically improved strains can affect both the timing and rate of antibiotic synthesis, and alter the regulation of antibiotic biosynthetic enzymes and enzymes involved in precursor metabolism. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2006-03-08 | E-GEOD-4395 | biostudies-arrayexpress
Project description:Mitochondrial fatty acid oxidation (FAO) is an important energy provider for cardiac work and changes in cardiac substrate preference are associated with different heart diseases. Carnitine palmitoyltransferase 1B (CPT1B) is thought to perform the rate limiting enzyme step in FAO and is inhibited by malonyl-CoA. The role of CPT1B in cardiac metabolism has been addressed by inhibiting or decreasing CPT1B protein or after modulation of tissue malonyl-CoA metabolism. We assessed the role of CPT1B malonyl-CoA sensitivity in cardiac metabolism.
2021-04-26 | GSE173256 | GEO
Project description:In the present study, we have used a genomic approach to understand how the classical mutate-and-screen method actually generated an improved rifamycin B producer. Compared with the reference strains Amycolatopsis mediterranei S699 (rifamycin B producer) and U32 (rifamycin SV producer), a total of 250 variations affecting a total of 227 coding sequences (CDS) were found in rifamycin B overproducing strain HP-130. One hundred nine CDS variations were specific to HP-130 as they were absent in both S699 and U32. A lot of variations affected genes coding for fatty acid (an lipid) metabolism, which is tightly interconnected with rifamycin biosynthesis by common metabolic precursors (malonyl-CoA, methylmalonyl-CoA). Interestingly, a nonsense mutation was mapped within mutB coding for methylmalonyl-CoA mutase suggesting the importance of metabolic re-direction of carbon flow toward rifamycin biosynthesis in the over-producing phenotype of HP-130. Other key mutations were: i.) a missense mutation affecting ppk, which encodes a polyphosphate kinase and was previously shown to play a negative role in the control of antibiotic biosynthesis in Streptomyces lividans; ii.) a missense mutation in argS2 affecting one of the two arginyl tRNA synthetases of A. mediterranei; iii.) a missense mutation in rifN coding for a protein belonging to the ROK family of transcriptional regulators with kanosamine kinase activity. Microarray analysis of the transcriptome of HP-130 as compared to that of S699 was useful to understand the effects of several mutations on global gene expression profile. Genomic and transcriptomic data were used to improve rifamycin B production in S699 by genetic engineering thus proving the causative effect of the above-mentioned mutations on the overproducing phenotype. In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of a rifamycin B overproducer (HP-130), which was obtained by the traditional mutate-and-screen method. To gain insight about the mechanisms underlying improved rifamycin B production in HP-130, DNA microarray of A. mediterranei were manufactured and used for comparative analysis of the gene expression profile in HP-130 and S699. In DNA microarray experiments the two strains were cultivated under standard batch-culture conditions in modified RFB 2244 fermentation medium, and samples were collected at different time points (24-72 h) for RNA extraction. Gene expression data were analyzed to identify transcripts modulated during the growth curve. Amycolatopsis mediterranei S699 (WT) and the improved rifamycin B producer (HP-130) were profiled at 5 time points. For each time point two biological replicates are provided.
2014-08-26 | E-GEOD-51015 | biostudies-arrayexpress
Project description:Fatty acid beta-oxidation (FAO), the breakdown of lipids, is a metabolic pathway used by various stem cells. FAO levels are generally high during quiescence and downregulated with proliferation. The endogenous metabolite malonyl-CoA modulates lipid metabolism as a reversible FAO inhibitor and as a substrate for de novo lipogenesis. Here we assessed whether malonyl-CoA can be exploited to steer the behavior of hematopoietic stem/progenitor cells (HSPCs), quiescent stem cells of clinical relevance. Treatment of mouse HSPCs in vitro with malonyl-CoA increases HSPC numbers compared to non-treated controls and ameliorates blood reconstitution capacity when transplanted in vivo, mainly through enhanced lymphoid reconstitution. Similarly, human HSPC numbers also increase upon malonyl-CoA treatment in vitro. These data corroborate that lipid metabolism can be targeted to direct cell fate and stem cell proliferation. Physiological modulation of metabolic pathways, rather than genetic or pharmacological inhibition, provides unique perspectives for stem cell manipulations in health and disease.
2020-08-25 | GSE153201 | GEO
Project description:Understanding and, ultimately, controlling the properties of amorphous materials is one of the key goals of material science. Among the different amorphous structures, a very important role is played by colloidal gels. It has been only recently understood that colloidal gels are the result of the interplay between phase separation and arrest. When short-ranged attractive colloids are quenched into the phase-separating region, density fluctuations are arrested and this results in ramified amorphous space-spanning structures that are capable of sustaining mechanical stress. We present a mechanism of aggregation through arrested demixing in binary colloidal mixtures, which leads to the formation of a yet unexplored class of materials--bigels. This material is obtained by tuning interspecies interactions. Using a computer model, we investigate the phase behavior and the structural properties of these bigels. We show the topological similarities and the geometrical differences between these binary, interpenetrating, arrested structures and their well-known monodisperse counterparts, colloidal gels. Our findings are supported by confocal microscopy experiments performed on mixtures of DNA-coated colloids. The mechanism of bigel formation is a generalization of arrested phase separation and is therefore universal.
| S-EPMC3511146 | biostudies-literature
Project description:Mlycd encodes malonyl-CoA decarboxylase (MCD), which is an enzyme that localizes in the cytosolic, mitochondrial, and peroxisomal compartments and catalyzes the conversion of malonyl-CoA into acetyl-CoA. Malonyl-CoA can be converted into malonylcarnitine (C3DC). Patients with an autosomal recessive defect of MCD and MCD KO mice have pronounced elevations of C3DC. Analysis of plasma C3DC levels in the BxD genetic reference population revealed increased levels in BxD strains that harbor the DBA/2J haplotype at the site of the Mlycd gene. RNA sequencing was performed on two samples of DBA/2J mouse livers and two C57BL/6J mouse livers. Decreased expression of Mlycd gene as well as intronic reads in intron 2 were observed in DBA/2J livers. Long-read sequecing of DBA/2J livers in the Mlycd region confirmed an intracisternal A-particle (IAP) retrotransposon in intron 2 of the DBA/2J Mlycd sequence. To confirm the causal nature of the variant, DBA/2J mice with and without the C57BL/6J variant of Mlycd spliced in were tested for products of MCD enzymatic activity, and the C57BL/6J variant was able to rescue the phenotype seen in the DBA/2J mice.
2024-10-26 | GSE186973 | GEO
Project description:In the present study, we have used a genomic approach to understand how the classical mutate-and-screen method actually generated an improved rifamycin B producer. Compared with the reference strains Amycolatopsis mediterranei S699 (rifamycin B producer) and U32 (rifamycin SV producer), a total of 250 variations affecting a total of 227 coding sequences (CDS) were found in rifamycin B overproducing strain HP-130. One hundred nine CDS variations were specific to HP-130 as they were absent in both S699 and U32. A lot of variations affected genes coding for fatty acid (an lipid) metabolism, which is tightly interconnected with rifamycin biosynthesis by common metabolic precursors (malonyl-CoA, methylmalonyl-CoA). Interestingly, a nonsense mutation was mapped within mutB coding for methylmalonyl-CoA mutase suggesting the importance of metabolic re-direction of carbon flow toward rifamycin biosynthesis in the over-producing phenotype of HP-130. Other key mutations were: i.) a missense mutation affecting ppk, which encodes a polyphosphate kinase and was previously shown to play a negative role in the control of antibiotic biosynthesis in Streptomyces lividans; ii.) a missense mutation in argS2 affecting one of the two arginyl tRNA synthetases of A. mediterranei; iii.) a missense mutation in rifN coding for a protein belonging to the ROK family of transcriptional regulators with kanosamine kinase activity. Microarray analysis of the transcriptome of HP-130 as compared to that of S699 was useful to understand the effects of several mutations on global gene expression profile. Genomic and transcriptomic data were used to improve rifamycin B production in S699 by genetic engineering thus proving the causative effect of the above-mentioned mutations on the overproducing phenotype.
2014-08-26 | GSE51015 | GEO
Project description:Fundamental alterations in lipid metabolism including increased rates of de novo lipogenesis (DNL), reduced fatty acid oxidation (FAOX) and ectopic lipid accumulation in skeletal muscle and liver are characteristic of type 2 diabetes mellitus (T2DM) and have been hypothesized to directly contribute to the molecular pathogenesis of the disease. Acetyl-CoA carboxylase (ACC) catalyzes the formation of malonyl-CoA, the rate limiting substrate for DML and key regulator of FAOX. ACC inhibitors have the potential to pharmacologically rebalance these metabolic alterations. In the present study, PF-04923503, a potent dual ACC1/ACC2 inhibitor with properties optimized for in vivo studies, suppressed levels of malonyl-CoA in primary hepatocytes, rat skeletal muscle ex vivo, as well as rat liver and skeletal muscle in vivo. This impact on malonyl-CoA was directly correlated (r2>0.9) with reduced hepatic DNL and inversely correlated with incresed rates of FAOX (r2>0.9). The pharmacological eccfect of PF-04923503 persisted with chronic treatment. High-fat fed rats treated with PF-04923503 for six weeks showed dose-dependent reductions in skeletal muscle and liver lipid accumulation. These changes correlated directly with markers for improved insulin sensitization. However, liver gene expression indicates that pharmacological inhibition results in compensation by up-regualtion of genes involved with DNL. These results suggest that pharmacological inhibition of ACC may have utility to help rebalance metabolic abnormalities in T2DM and improve insulin sensitivity. Differential gene expression was assessed by Affymetrix microarray experiments for 15 liver samples across 3 pharmacological treatment groups (vehicle control 0.5% methylcellulose had 5 samples, PF-04923503 10mpk had 5 samples, PF-04923503 30mpk had 5 samples)
2011-06-30 | E-GEOD-28058 | biostudies-arrayexpress