Comparative omics analysis guides to further enhance the biosynthesis of erythromycin by an overproducer

Omics approaches have succeeded in understanding the boosted productivity of natural products by industrial high-producing microorganisms. Here, with the updated genome sequence and transcriptomic profiles derived from next-generation high throughput sequencing, we exploited comparative omics analysis to further enhance the biosynthesis of erythromycin in an industrial overproducer, Saccharopolyspora erythraea HL3168 E3. By comparing the genome of E3 with the wild type NRRL23338, we identified large deletions of 30 kilobases in total located inside coding sequences and 255 single nucleotide polymorphisms over the whole genome of E3. A large amount of genomic variation was observed in genes responsible for pathways which supply precursors, cofactors and signals for the biosynthesis of erythromycin. Transcriptional analysis revealed 2-oxoglutarate and L-glutamine/L-glutamate as reporter metabolites to distinguish the two strains. Around the node of 2-oxoglutarate, also genomic mutations were observed. Furthermore, the transcriptomic data suggested that genes involved in the biosynthesis of erythromycin were significantly up-regulated constantly, whereas some genes in the biosynthesis clusters of other secondary metabolites contained nonsense mutations and were expressed at extremely low levels. Based on the omics analysis, readily available strategies were proposed to engineer E3 by simultaneously overexpressing sucB (coding for 2-oxoglutarate dehydrogenase E2 component) and sucA (coding for 2-oxoglutarate dehydrogenase E1 component), which increased the erythromycin titer by 45% compared to E3 in batch culture. This work provides more promising molecular targets to engineer for enhancement of erythromycin production. Overall design: S.erythraea NRRL23338 cultivated in the minimal liquid medium was harvested both at exponential phase and stationary phase (10 h & 50 h). The total RNA were sequenced in duplicate.