Dataset Information

Proteomic study of S erythrea bioprocess

ABSTRACT: Proteome composition of Saccharopolyspora erythrea during the fermentation bioprocess was studied. Samples were collected at two timepoints (prior to the rapid growth phase and at the start of the rapid growth phase), and relative differences in protein abundance were determined by spectral counting.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Saccharopolyspora Erythraea (streptomyces Erythraeus)

TISSUE(S): Cell Suspension Culture

SUBMITTER: Marko Fonovic

LAB HEAD: Marko Fonovic

PROVIDER: PXD002472 | Pride | 2016-05-26

REPOSITORIES: Pride

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Publications

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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Project description:We describe a simple method, Digital Restriction Enzyme Analysis of Methylation (DREAM), based on sequential DNA digestion with a pair of methylation-blocked and methylation-tolerant neoschizomeric restriction enzymes SmaI/XmaI followed by end repair and ultra-deep sequencing. DREAM provides information on 160,000 unique CpG sites of which 39,000 are in CpG islands, and 33,000 are at transcription start sites (-1 kb to +1 kb) of 13,139 RefSeq genes. We compared DNA methylation values in white blood cells from 4 healthy individuals and found them to be remarkably uniform. Interindividual differences >30% were observed only at 227 of 28,331 (0.8%) of autosomal CCCGGG sites covered by 100+ sequencing reads. Similarly, differences at only 59 sites were observed between the cord and adult blood. Conserved methylation patterns in healthy blood cells contrasted with extensive changes affecting 18-40% of CpG sites in leukemia. The method is cost effective, quantitative (r2=0.93 when compared to bisulfite pyrosequencing), reproducible (r2=0.997), and can detect differences >25% with false positive rate <0.001. Accurate analysis of changes in DNA methylation will be useful in quantifying epigenetic effects of environment and nutrition, correlating developmental epigenetic variation with phenotypes, understanding epigenetics of cancer and chronic diseases, measuring the effects of drugs on DNA methylation or deriving new biological insights into mammalian genomes. Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the DNA methylation profiles of healthy white blood cells from cord blood and adult blood, acute myeloid leukemia bone marrow, and two leukemia cell lines (HEL and K562). In this approach, genomic DNA is sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represent methylation status of the CCCGGG sites. These end sequences are analyzed by next-generation sequencing, and thereafter the methylation status at individual CCCGGG sites across the genome can be determined.

Dataset Information

Proteomic study of S erythrea bioprocess

Publications

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

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