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Finding new pathway-specific regulators by clustering method using threshold standard deviation based on DNA chip data of Streptomyces coelicolor

  • Genomics and Proteomics
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Abstract

In order to identify the regulators involved in antibiotic production or time-specific cellular events, the messenger ribonucleic acid (mRNA) expression data of the two gene clusters, actinorhodin (ACT) and undecylprodigiosin (RED) biosynthetic genes, were clustered with known mRNA expression data of regulators from S. coelicolor using a filtering method based on standard deviation and clustering analysis. The result identified five regulators including two well-known regulators namely, SCO3579 (WlbA) and SCO6722 (SsgD). Using overexpression and deletion of the regulator genes, we were able to identify two regulators, i.e., SCO0608 and SCO6808, playing roles as repressors in antibiotics production and sporulation. This approach can be easily applied to mapping out new regulators related to any interesting target gene clusters showing characteristic expression patterns. The result can also be used to provide insightful information on the selection rules among a large number of regulators.

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Acknowledgments

We thank the John Innes Center for providing the cosmid library. This work was partially supported by the Korea Science and Engineering Foundation (KOSEF) Grant funded by the Korea Government (MOST; no. R01-2006-000-10234-0) and a grant (Code no. KRF-2005-005-J16002) from Korea Research Foundation, Republic of Korea.

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Authors and Affiliations

  1. School of Chemical and biological Engineering, Seoul National University, Seoul, South Korea

    Yung-Hun Yang, Ji-Nu Kim, Eunjung Song, Eunjung Kim & Byung-Gee Kim

  2. Institute of Bioengineering, Seoul National University, Seoul, South Korea

    Yung-Hun Yang, Ji-Nu Kim, Eunjung Song, Eunjung Kim & Byung-Gee Kim

  3. Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, South Korea

    Min-Kyu Oh

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  1. Yung-Hun Yang
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Correspondence to Byung-Gee Kim.

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Yang, YH., Kim, JN., Song, E. et al. Finding new pathway-specific regulators by clustering method using threshold standard deviation based on DNA chip data of Streptomyces coelicolor . Appl Microbiol Biotechnol 80, 709–717 (2008). https://doi.org/10.1007/s00253-008-1574-3

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