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A genome-wide transcriptomic analysis reveals diverse roles of the two-component system DraR-K in the physiological and morphological differentiation of Streptomyces coelicolor

  • Genomics, transcriptomics, proteomics
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Abstract

A novel two-component system (TCS) of DraR-K was previously identified as playing differential roles in the biosynthesis of antibiotics (blue-pigmented type II polyketide actinorhodin (ACT), red-pigmented tripyrrole undecylprodigiosin (RED), and yellow-pigmented type I polyketide (yCPK)) in Streptomyces coelicolor M145 under the conditions of minimal medium (MM) supplemented with a high concentration of different nitrogen sources (e.g., 75 mM glutamine). To assess whether DraR-K has more globalized roles, a genome-wide transcriptomic analysis of the parental strain M145 and a ΔdraR-K mutant under the condition of MM supplemented with 75 mM glutamine was performed using DNA microarray analysis combined with real-time reverse transcriptase PCR (RT-qPCR). The analyses showed that deletion of the draR-K genes led to the differential expression not only of the biosynthetic gene clusters of ACT, RED, and yCPK but also of other five secondary metabolite biosynthetic clusters. In addition, a number of primary metabolism-related genes in the ΔdraR-K mutant, such as ureA/B/C/D/G/F, the pstSCAB operon, and the chb gene, exhibited altered expression, which might enable the organism to balance the C/N/P ratio under the condition of a high concentration of glutamine. We also found that the expression of many developmental genes, including ramR, chpA/D/E, and the whiE gene cluster, was affected by the draR-K deletion. Furthermore, the direct role of DraR-K on the transcription of several genes, including chb and pepA/pepA2, was validated using electrophoretic mobility shift assays (EMSAs). In summary, our transcriptomic analyses revealed that DraR-K plays global regulatory roles in the physiological and morphological differentiation of S. coelicolor.

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Acknowledgments

This work was supported by the National High Technology Research and Development Program of China (2012AA022107), National Basic Research Program of China (2012CB721103), and National Natural Science Foundation of China (31121001, 31370081, and 31430004). The authors gratefully acknowledge the support of SA-SIBS scholarship program and TOLO Biotechnology (Shanghai, China) for their excellent assistance in DNase I footprinting assay.

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  1. Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People’s Republic of China

    Zhenyu Yu, Hong Zhu, Guosong Zheng, Weihong Jiang & Yinhua Lu

  2. Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, 200237, People’s Republic of China

    Weihong Jiang

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  1. Zhenyu Yu
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  2. Hong Zhu
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  3. Guosong Zheng
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Yu, Z., Zhu, H., Zheng, G. et al. A genome-wide transcriptomic analysis reveals diverse roles of the two-component system DraR-K in the physiological and morphological differentiation of Streptomyces coelicolor . Appl Microbiol Biotechnol 98, 9351–9363 (2014). https://doi.org/10.1007/s00253-014-6102-z

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