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

Yung Hun Yang, Ji Nu Kim, Eunjung Song, Eunjung Kim, Min-Kyu Oh, Byung Gee Kim

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)709-717
Number of pages9
JournalApplied Microbiology and Biotechnology
Volume80
Issue number4
DOIs
Publication statusPublished - 2008 Sep 1

Fingerprint

Streptomyces coelicolor
Multigene Family
Oligonucleotide Array Sequence Analysis
Cluster Analysis
DNA
Genes
RNA
Anti-Bacterial Agents
Antibiotics
Regulator Genes
undecylprodigiosin
actinorhodin

Keywords

  • Clustering
  • DNA chip
  • Pathway-specific regulator
  • Standard deviation
  • Streptomyces coelicolor

ASJC Scopus subject areas

  • Biotechnology
  • Microbiology
  • Bioengineering
  • Microbiology (medical)

Cite this

Finding new pathway-specific regulators by clustering method using threshold standard deviation based on DNA chip data of Streptomyces coelicolor. / Yang, Yung Hun; Kim, Ji Nu; Song, Eunjung; Kim, Eunjung; Oh, Min-Kyu; Kim, Byung Gee.

In: Applied Microbiology and Biotechnology, Vol. 80, No. 4, 01.09.2008, p. 709-717.

Research output: Contribution to journalArticle

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AU - Oh, Min-Kyu

AU - Kim, Byung Gee

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