Chowdhury Nilkanta, Bagchi Angshuman
Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, India.
Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, India.
Gene. 2016 Apr 10;580(1):80-7. doi: 10.1016/j.gene.2015.12.067. Epub 2016 Jan 6.
Pseudomonas aeruginosa is an opportunistic human pathogen. This organism attacks human patients suffering from diseases like AIDS, cancer, cystic fibrosis, etc. One of the important virulent factors produced by this organism is Hydrogen Cyanide. This is expressed from the genes encoded by the hcnABC operon. The expressions of the genes encoded by hcnABC operon are mediated mainly by the interactions of LasR protein with the corresponding promoter region of the hcnABC operon. The LasR protein acts as a dimer and binds to the promoter DNA with the help of an autoinducer ligand. However, till date the detailed molecular mechanism of how the LasR protein interacts with the promoter DNA is not clearly known. Therefore, in this work, an attempt has been made to analyze the mode of interactions of the LasR protein with the promoter DNA region of the hcnABC operon. We analyzed the three dimensional structure of the LasR protein from Pseudomonas aeruginosa and docked the protein with the autoinducer ligand. We then docked the ligand-bound-LasR-protein as well the LasR-protein-without-the-autoinducer-ligand on to the promoter DNA region of hcnABC operon. We analyzed the details of the interaction profiles of LasR protein with the autoinducer ligand. We also deciphered the details of the LasR promoter-DNA interactions. We compared the modes of DNA bindings by the LasR protein in presence and absence of the autoinducer ligand and tried to analyze the molecular details of the binding of LasR protein with the promoter DNA region of hcnABC operon during hcnABC gene expression. This study may therefore pave the pathway for future experiments to determine the relative effects of the amino acid residues of LasR protein in DNA binding during the transcription of hcnABC operon.
铜绿假单胞菌是一种机会性人类病原体。这种微生物会侵袭患有艾滋病、癌症、囊性纤维化等疾病的人类患者。该微生物产生的重要致病因素之一是氰化氢。它由hcnABC操纵子编码的基因表达。hcnABC操纵子编码基因的表达主要由LasR蛋白与hcnABC操纵子相应启动子区域的相互作用介导。LasR蛋白以二聚体形式发挥作用，并借助自诱导配体与启动子DNA结合。然而，迄今为止，LasR蛋白与启动子DNA相互作用的详细分子机制尚不清楚。因此，在这项工作中，我们试图分析LasR蛋白与hcnABC操纵子启动子DNA区域的相互作用模式。我们分析了铜绿假单胞菌LasR蛋白的三维结构，并将该蛋白与自诱导配体进行对接。然后，我们将结合配体的LasR蛋白以及未结合自诱导配体的LasR蛋白对接至hcnABC操纵子的启动子DNA区域。我们分析了LasR蛋白与自诱导配体相互作用图谱的细节。我们还解读了LasR与启动子DNA相互作用的细节。我们比较了有和没有自诱导配体时LasR蛋白与DNA的结合模式，并试图分析在hcnABC基因表达过程中LasR蛋白与hcnABC操纵子启动子DNA区域结合的分子细节。因此，这项研究可能为未来的实验铺平道路，以确定在hcnABC操纵子转录过程中LasR蛋白的氨基酸残基在DNA结合中的相对作用。
