RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor.
RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor.
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DOI：
10.1371/journal.pone.0106181
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Chander M
中科院分区：
文献类型：
--
作者：
Naseer N;Shapiro JA;Chander M
氧化还原调节转录因子SoxR在不同的细菌中是保守的，但新的研究表明，这种蛋白质在不同的细菌中起着不同的生理作用。SoxR调节大肠杆菌和相关肠道菌对外源性氧化还原循环药物的整体氧化应激反应（涉及>100个基因）。然而，在抗生素生产商天蓝色链霉菌和铜绿假单胞菌中，SoxR调控的基因数量较少，这些基因编码膜转运蛋白和与抗生素剪裁酶同源的蛋白质。在S.在天蓝色假单胞菌和铜绿假单胞菌中，SoxR调节的基因在内源性产生的氧化还原活性抗生素的生产过程中在稳定期表达。这些观察结果表明，SoxR进化到感应内源性次级代谢产物，并激活机器来处理和运输它们。先前的生物信息学分析在基因组中搜索假定启动子中的SoxR结合位点，确定了S.腔棘鱼包括ABC转运蛋白、两种氧化还原酶、单加氧酶和差向异构酶/脱氢酶。由于这种计算机筛选可能错过了潜在的SoxR靶点，我们对野生型S. coelicolor和soxR缺陷突变体在稳定期使用RNA-Seq.我们的分析揭示了S.编码一种推定的醌氧化还原酶的腔棘鱼。了解SoxR调控的基因的完整互补性将有助于研究阐明这种调控分子在抗生素生产中的功能。
The redox-regulated transcription factor SoxR is conserved in diverse bacteria, but emerging studies suggest that this protein plays distinct physiological roles in different bacteria. SoxR regulates a global oxidative stress response (involving >100 genes) against exogenous redox-cycling drugs in Escherichia coli and related enterics. In the antibiotic producers Streptomyces coelicolor and Pseudomonas aeruginosa, however, SoxR regulates a smaller number of genes that encode membrane transporters and proteins with homology to antibiotic-tailoring enzymes. In both S. coelicolor and P. aeruginosa, SoxR-regulated genes are expressed in stationary phase during the production of endogenously-produced redox-active antibiotics. These observations suggest that SoxR evolved to sense endogenous secondary metabolites and activate machinery to process and transport them in antibiotic-producing bacteria. Previous bioinformatics analysis that searched the genome for SoxR-binding sites in putative promoters defined a five-gene SoxR regulon in S. coelicolor including an ABC transporter, two oxidoreductases, a monooxygenase and an epimerase/dehydratase. Since this in silico screen may have missed potential SoxR-targets, we conducted a whole genome transcriptome comparison of wild type S. coelicolor and a soxR-deficient mutant in stationary phase using RNA-Seq. Our analysis revealed a sixth SoxR-regulated gene in S. coelicolor that encodes a putative quinone oxidoreductase. Knowledge of the full complement of genes regulated by SoxR will facilitate studies to elucidate the function of this regulatory molecule in antibiotic producers.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
3.6
作者：
Dietrich, Lars E. P.;Price-Whelan, Alexa;Newman, Dianne K.
通讯作者：
Newman, Dianne K.
影响因子：
14.9
作者：
AMABILECUEVAS, CF;DEMPLE, B
通讯作者：
DEMPLE, B
影响因子：
3.2
作者：
Dela Cruz, Rica;Gao, Yang;Chander, Monica
通讯作者：
Chander, Monica