title: Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains.
abstract: BACKGROUND
  S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level.
  
  
  RESULTS
  We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data.
  
  
  CONCLUSIONS
  This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future.
authors.forename: Yuan-Yuan
authors.initials: YY
authors.lastname: Li
authors.forename: Xiao
authors.initials: X
authors.lastname: Chang
authors.forename: Wen-Bang
authors.initials: WB
authors.lastname: Yu
authors.forename: Hao
authors.initials: H
authors.lastname: Li
authors.forename: Zhi-Qiang
authors.initials: ZQ
authors.lastname: Ye
authors.forename: Hui
authors.initials: H
authors.lastname: Yu
authors.forename: Bao-Hong
authors.initials: BH
authors.lastname: Liu
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Si-Liang
authors.initials: SL
authors.lastname: Zhang
authors.forename: Bang-Ce
authors.initials: BC
authors.lastname: Ye
authors.forename: Yi-Xue
authors.initials: YX
authors.lastname: Li
mesh_terms: D055028:Comparative Genomic Hybridization; D004917:Erythromycin / Q000096:biosynthesis*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D016930:Saccharopolyspora / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D004917:Erythromycin
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