Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains

BMC Genomics

Research Article

Wen-Bang Yu¹  Yan Zhang¹  Si-Liang Zhang¹  Hao Li¹  Bao-Hong Liu²  Yuan-Yuan Li²  Yi-Xue Li³  Hui Yu³  Xiao Chang⁴  Bang-Ce Ye⁵  Zhi-Qiang Ye⁶ 

[1] Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 200237, Shanghai, China;Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, 201203, Shanghai, China;Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, 201203, Shanghai, China;Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China;Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, 201203, Shanghai, China;Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China;The Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, PA 19104, Philadelphia, USA;Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, 201203, Shanghai, China;Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 200237, Shanghai, China;Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, 201203, Shanghai, China;Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China;

关键词: S. erythraea;    Erythromycin biosynthesis;    Functional comparative genetics;    Regulation mechanism;   

DOI  :  10.1186/1471-2164-14-523

 received in 2013-04-23, accepted in 2013-07-26,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundS. 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.ResultsWe 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.ConclusionThis 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.

【 授权许可】

CC BY   
© Li et al.; licensee BioMed Central Ltd. 2013