Conclusions
In the present study, we re-sequenced the whole genome of an erythromycin overproducer S. erythraea HL3168 E3 and carried out comparative genomic and transcriptomic analysis of E3 with respect to the wild type NRRL23338. Genomic variations occurred in E3 in terms of gene transposition, fragment deletions in 56 sequences and 255 SNPs, which were partly distinguished from a previous E3 genome obtained via pyrosequencing (Y. Li et al., 2013). Comparative omics analysis revealed that the phenotypic difference between E3 and NRRL23338 resulted mainly from genomic and transcriptomic changes in central carbon and nitrogen metabolism, biosynthesis of secondary metabolites, and cofactor metabolism.
Within transcriptomic analysis the top ranking reporter metabolites were L-glutamine/L-glutamate and 2-oxoglutarate, which pointed to the important role of nitrogen metabolism and the signal transduction in the biosynthesis of erythromycin. Genes coding for direct regulators of erythromycin biosynthesis gene cluster i.e. BldD and PhoP in E3 were not stimulated, we predicted that the regulatory networks of erythromycin BGC in E3 might be different from our anticipation. Expression of genes involved in the TCA cycle, ED pathway and the degradation of fatty acid changed in E3, which facilitated to supply more precursors for the biosynthesis of erythromycin. Moreover, several genes involved in biosynthesis of secondary metabolites other than erythromycin were expressed at extremely low levels in E3, which addressed the importance of construction of super-producer through genome minimization (Peano et al., 2007).
Based on the omics analysis, we proposed putative mechanisms by which E3 boosted the biosynthesis of erythromycin. The mechanisms provided molecular targets to strengthen the productivity of erythromycin by E3. As an example, we enhanced the supply of erythromycin precursors by manipulating targets derived from one of the proposed mechanisms. The overexpression of sucBA resulted in an enhancement of the erythromycin titer by 71% in E3. The present study showed that comparative omics analysis could reveal the differences between the physiologies of wild type strains and their overproducing derivatives, and also point out strategies for enhancing the production of secondary metabolites in overproducers even further.