title: Finding new pathway-specific regulators by clustering method using threshold standard deviation based on DNA chip data of Streptomyces coelicolor.
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.
authors.affiliation: School of Chemical and biological Engineering, Seoul National University, Seoul, South Korea.
authors.forename: Yung-Hun
authors.initials: YH
authors.lastname: Yang
authors.forename: Ji-Nu
authors.initials: JN
authors.lastname: Kim
authors.forename: Eunjung
authors.initials: E
authors.lastname: Song
authors.forename: Eunjung
authors.initials: E
authors.lastname: Kim
authors.forename: Min-Kyu
authors.initials: MK
authors.lastname: Oh
authors.forename: Byung-Gee
authors.initials: BG
authors.lastname: Kim
mesh_terms: D000880:Anthraquinones / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D016000:Cluster Analysis; D005809:Genes, Regulator; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D011353:Prodigiosin / Q000031:analogs & derivatives / Q000378:metabolism; D017384:Sequence Deletion; D048372:Streptomyces coelicolor / Q000235:genetics* / Q000378:metabolism*; D000095622:Benzoisochromanequinones
chemical_list: D000880:Anthraquinones; D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D011353:Prodigiosin; C047347:undecylprodigiosin; C013390:actinorhodin; D000095622:Benzoisochromanequinones