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

被引：9

作者：

Yang, Yung-Hun ^{[1
,2
]}

Kim, Ji-Nu ^{[1
,2
]}

Song, Eunjung ^{[1
,2
]}

Kim, Eunjung ^{[1
,2
]}

Oh, Min-Kyu ^{[3
]}

Kim, Byung-Gee ^{[1
,2
]}

机构：

[1] Seoul Natl Univ, Sch Chem & Biol Engn, Seoul, South Korea

[2] Seoul Natl Univ, Inst Bioengn, Seoul, South Korea

[3] Korea Univ, Dept Chem & Biol Engn, Coll Engn, Seoul, South Korea

来源：

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY | 2008年 / 80卷 / 04期

关键词：

Streptomyces coelicolor; DNA chip; clustering; standard deviation; pathway-specific regulator;

D O I：

10.1007/s00253-008-1574-3

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页码：709 / 717

页数：9