Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae
Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae
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DtxR 调节子的预测：白喉棒杆菌中白喉毒素阻遏物控制的结合位点和操纵子的鉴定
作者：
Sailu Yellaboina;Sarita Ranjan;P. Chakhaiyar;S. Hasnain;A. Ranjan
背景白喉棒状杆菌的白喉毒素阻遏蛋白 DtxR 已被证明是一种铁激活的转录调节因子，不仅控制白喉毒素的表达，还控制铁摄取基因的表达。本研究旨在鉴定DtxR控制的假定结合位点和操纵子，以了解DtxR在白喉棒状杆菌病理生理学中的作用。结果采用位置香农相对熵方法构建DtxR结合位点识别图谱，并用于鉴定白喉棒状杆菌基因组中DtxR的假定调控位点。此外，考虑到预测的 DtxR 调控位点和基因组注释，还确定了 DtxR 调控的操纵子。很少有预测的基序通过电泳迁移率变动测定进行实验验证。该分析确定了编码甲酰胺嘧啶-DNA糖基化酶（FpG）的新型铁调节基因上游的基序，FpG是一种参与DNA修复和饥饿诱导DNA结合蛋白（Dps）的酶，Dps参与铁储存和氧化应激防御。此外，我们还发现了编码分选酶基因上游的 DtxR 基序，分选酶催化宿主相互作用蛋白锚定到病原菌的细胞壁上，以及分泌系统的蛋白质，可能参与包括白喉毒素在内的各种铁调节毒力因子的易位。结论我们使用计算机方法鉴定了白喉棒杆菌中由 DtxR 控制的推定结合位点和基因。我们的分析表明，DtxR 可以在 Fe+2 诱导的芬顿反应和保护 DNA 免受氧化损伤之间提供分子联系。 DtxR 调节的 Dps 可防止 Fe+2 和 H2O2 的致命结合，并通过非特异性 DNA 结合来保护 DNA。此外，DtxR 可以通过调节分选酶、潜在候选疫苗和分泌系统蛋白质的水平，在宿主相互作用和毒力中发挥重要作用。
BackgroundThe diphtheria toxin repressor, DtxR, of Corynebacterium diphtheriae has been shown to be an iron-activated transcription regulator that controls not only the expression of diphtheria toxin but also of iron uptake genes. This study aims to identify putative binding sites and operons controlled by DtxR to understand the role of DtxR in patho-physiology of Corynebacterium diphtheriae.ResultPositional Shannon relative entropy method was used to build the DtxR-binding site recognition profile and the later was used to identify putative regulatory sites of DtxR within C. diphtheriae genome. In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation. Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay. The analysis identifies motifs upstream to the novel iron-regulated genes that code for Formamidopyrimidine-DNA glycosylase (FpG), an enzyme involved in DNA-repair and starvation inducible DNA-binding protein (Dps) which is involved in iron storage and oxidative stress defense. In addition, we have found the DtxR motifs upstream to the genes that code for sortase which catalyzes anchoring of host-interacting proteins to the cell wall of pathogenic bacteria and the proteins of secretory system which could be involved in translocation of various iron-regulated virulence factors including diphtheria toxin.ConclusionsWe have used an in silico approach to identify the putative binding sites and genes controlled by DtxR in Corynebacterium diphtheriae. Our analysis shows that DtxR could provide a molecular link between Fe+2-induced Fenton's reaction and protection of DNA from oxidative damage. DtxR-regulated Dps prevents lethal combination of Fe+2 and H2O2 and also protects DNA by nonspecific DNA-binding. In addition DtxR could play an important role in host interaction and virulence by regulating the levels of sortase, a potential vaccine candidate and proteins of secretory system.
DOI：
10.1016/s0021-9258(19)36677-3
发表时间：
1992-10
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
X. Tao;J. Murphy
通讯作者：
X. Tao;J. Murphy
枯草芽孢杆菌 spc-alpha 区域的遗传和转录组织。
影响因子：
3.5
作者：
Suh,JW;Boylan,SA;Oh,SH;Price,CW
通讯作者：
Price,CW