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Saccharopolyspora erythraea NRRL 2338 strain:DSM 40517 | isolate:DSM 40517

ABSTRACT: Saccharopolyspora erythraea DSM 40517 genome sequencing

PROVIDER: PRJNA323074 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR4181397_subreads.fastq.gz	Fastqsanger.gz
	SRR4181398_subreads.fastq.gz	Fastqsanger.gz
	SRR4181399_subreads.fastq.gz	Fastqsanger.gz

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Complete Gene Expression Profiling of Saccharopolyspora erythraea NRRL 2338

Project description:A DNA microarray was designed and constructed using the genome sequence of Saccharopolyspora erythraea strain NRRL 2338. Following growth in liquid medium, we analysed the expression of 6494 ORFs along the time course. The results indicated that the 404 genes, whose expression significatively correlated with the time course, identify three distinct growth phases: a rapid growth until 32 h (phase A); a growth slowdown until 52 h (phase B); another rapid growth phase from 56 h to 72 h (phase C) before entering the stationary phase. We experimentally determined regional organization of transcription along the chromosome, highlighting differences between core and non-core regions, but also strand specific patterns of expression, and the behavior of major functional classes. Temporal expression of all the gene clusters for secondary metabolism was analyzed, confirming ery cluster up-regulation during the first growth phase, and finding out six secondary metabolism clusters that are clearly regulated during growth. The use of a DNA microarray, specifically designed on the Sac. erythraea genome sequence, improved specificity and sensitivity of gene expression analysis, giving a global and at the same time detailed picture of how Sac. erythraea genes are modulated. Keywords: time course

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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.

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Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea

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Project description:Saccharopolyspora erythraea Raw sequence reads

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Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain.

Project description:BACKGROUND: The molecular mechanisms altered by the traditional mutation and screening approach during the improvement of antibiotic-producing microorganisms are still poorly understood although this information is essential to design rational strategies for industrial strain improvement. In this study, we applied comparative genomics to identify all genetic changes occurring during the development of an erythromycin overproducer obtained using the traditional mutate-and- screen method. RESULTS: Compared with the parental Saccharopolyspora erythraea NRRL 2338, the genome of the overproducing strain presents 117 deletion, 78 insertion and 12 transposition sites, with 71 insertion/deletion sites mapping within coding sequences (CDSs) and generating frame-shift mutations. Single nucleotide variations are present in 144 CDSs. Overall, the genomic variations affect 227 proteins of the overproducing strain and a considerable number of mutations alter genes of key enzymes in the central carbon and nitrogen metabolism and in the biosynthesis of secondary metabolites, resulting in the redirection of common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, affect global expression profile as demonstrated by a comparative analysis of the parental and overproducer expression profiles. Genomic data, finally, suggest that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes. CONCLUSIONS: This study helps to clarify the mechanisms underlying antibiotic overproduction providing valuable information about new possible molecular targets for rationale strain improvement.

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Saccharopolyspora erythraea

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Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea

Project description:We report the effect of addition of N-acetylglucosamine in Saccharopolyspora erythraea reactor cultures on the transcription of genes related to dasR regulon Examination of one time-point after 45 minutes of the addition of N-acetylglucosamine in reactor cultures.

2014-04-15 | E-GEOD-56541 | biostudies-arrayexpress

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