In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection.
In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection.
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DOI：
10.1186/gb-2004-5-2-r9
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发表时间：
2004
期刊：
影响因子：
12.3
通讯作者：
De Moor B
中科院分区：
文献类型：
--
作者：
Marchal K;De Keersmaecker S;Monsieurs P;van Boxel N;Lemmens K;Thijs G;Vanderleyden J;De Moor B
对鼠伤寒沙门氏菌中PmrA转录因子靶标的全基因组计算筛选发现了新的靶标基因。PmrAB(BasSR)双组分调控系统是鼠伤寒沙门氏菌毒力所必需的。PmrAB控制的脂多糖(LPS)层的修饰对阳离子抗生素多肽具有抵抗力，这可能允许细菌在巨噬细胞内生存。PmrAB系统也能抵抗Fe3+介导的杀伤。最近发现了该系统的新靶点，这些靶点似乎在PmrAB已被描述的功能中没有作用，这表明PmrAB依赖的调节子可能包含额外的、未识别的靶点。我们对PmrAB系统的可能靶点进行了电子计算机分析。利用DNA中PmrA结合位点的基序模型，进行全基因组筛选以检测PmrAB靶基因。为了增加对预测的信心，使用基于Gibbs抽样的基序检测程序对所有假定的目标进行了跨物种比较(系统发育足迹)。除了已知的目标，我们还检测到了功能未知的其他目标。其中四种药物(aybD、aroq、mig-13和ssej)得到了实验验证。对YYBD中PmrA结合位点(PmrA盒)的定点突变揭示了特定的序列要求。我们通过恢复大多数已知的依赖于PmrAB的目标和识别我们能够在实验中验证的未知目标来展示我们程序的效率。我们还明确了进一步研究的方向，以帮助阐明鼠伤寒沙门氏菌的毒力途径。
A genome-wide computational screen for targets of the PmrA transcription factor in Salmonella typhimurium has identified novel target genes. The PmrAB (BasSR) two-component regulatory system is required for Salmonella typhimurium virulence. PmrAB-controlled modifications of the lipopolysaccharide (LPS) layer confer resistance to cationic antibiotic polypeptides, which may allow bacteria to survive within macrophages. The PmrAB system also confers resistance to Fe3+-mediated killing. New targets of the system have recently been discovered that seem not to have a role in the well-described functions of PmrAB, suggesting that the PmrAB-dependent regulon might contain additional, unidentified targets. We performed an in silico analysis of possible targets of the PmrAB system. Using a motif model of the PmrA binding site in DNA, genome-wide screening was carried out to detect PmrAB target genes. To increase confidence in the predictions, all putative targets were subjected to a cross-species comparison (phylogenetic footprinting) using a Gibbs sampling-based motif-detection procedure. As well as the known targets, we detected additional targets with unknown functions. Four of these were experimentally validated (yibD, aroQ, mig-13 and sseJ). Site-directed mutagenesis of the PmrA-binding site (PmrA box) in yibD revealed specific sequence requirements. We demonstrated the efficiency of our procedure by recovering most of the known PmrAB-dependent targets and by identifying unknown targets that we were able to validate experimentally. We also pinpointed directions for further research that could help elucidate the S. typhimurium virulence pathway.
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影响因子：
3.2
作者：
Brodsky, IE;Ernst, RK;Falkow, S
通讯作者：
Falkow, S
影响因子：
3.6
作者：
Gunn, JS;Lim, KB;Miller, SI
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作者：
Kox, LFF;Wösten, MMSM;Groisman, EA
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Groisman, EA
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14.9
作者：
Benson, DA;Karsch-Mizrachi, I;Wheeler, DL
通讯作者：
Wheeler, DL
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作者：
Breazeale, SD;Ribeiro, AA;Raetz, CRH
通讯作者：
Raetz, CRH