Finding new pathway-specific regulators by clustering method using threshold standard deviation based on DNA chip data of Streptomyces coelicolor.
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.
Yang
Yung-Hun
YH
School of Chemical and biological Engineering, Seoul National University, Seoul, South Korea.
Kim
Ji-Nu
JN
Song
Eunjung
E
Kim
Eunjung
E
Oh
Min-Kyu
MK
Kim
Byung-Gee
BG
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
D000880:Anthraquinones; D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D011353:Prodigiosin; C047347:undecylprodigiosin; C013390:actinorhodin; D000095622:Benzoisochromanequinones