Combined In Silico and In Vitro Study to Reveal the Structural Insights and Nucleotide-Binding Ability of the Transcriptional Regulator PehR from the Phytopathogen Ralstonia solanacearum.

Abstract

The transcriptional regulator PehR regulates the synthesis of the extracellular plant cell wall-degrading enzyme polygalacturonase, which is essential in the bacterial wilt of plants caused by one of the most devastating plant phytopathogens, Ralstonia solanacearum. The bacterium has a wide global distribution infecting many different plant species, resulting in massive agricultural and economic losses. Because the PehR molecular structure has not yet been determined and the structural consequences of PehR on ligand binding have not been thoroughly investigated, we have used an in silico approach combined with in vitro experiments for the first time to characterize the PehR regulator from a local isolate (Tezpur, Assam, India) of the phytopathogenic bacterium R. solanacearum F1C1. In this study, an in silico approach was employed to model the 3D structure of the PehR regulator, followed by the binding analysis of different ligands against this regulatory protein. Molecular docking studies suggest that ATP has the highest binding affinity for the PehR regulator. By using molecular dynamics (MD) simulation analysis, involving root-mean-square deviation, root-mean-square fluctuations, hydrogen bonding, radius of gyration, solvent-accessible surface area, and principal component analysis, it was possible to confirm the sudden conformational changes of the PehR regulator caused by the presence of ATP. We used an in vitro approach to further validate the formation of the PehR-ATP complex. In this approach, recombinant DNA technology was used to clone, express, and purify the gene encoding the PehR regulator from R. solanacearum F1C1. Purified PehR was used in ATP-binding experiments using fluorescence spectroscopy and Fourier transform infrared spectroscopy, the outcomes of which showed a potent binding to ATP. The putative PehR-ATP-binding analysis revealed the importance of the amino acids Lys190, Glu191, Arg192, Arg375, and Asp378 for the ATP-binding process, but further study is required to confirm this. It will be simpler to comprehend the catalytic mechanisms of a crucial PehR regulator process in R. solanacearum with the aid of the ATP-binding process hints provided by these structural biology applications.