Unveiling preferred chemoattractants for rhizosphere PGPR colonization by molecular docking and molecular dynamics simulations

Unveiling the preferred chemoattractants of plant growth-promoting rhizobacteria (PGPR) toward the rhizosphere is crucial for engineering PGPR to improve their chemotactic rhizocompetence. Here, we selected 59 common components of root exudates and calculated the binding free energies between the components and the ligand-binding domains (LBDs) of 15 annotated chemoreceptors with extracellular LBDs in the genome of the PGPR strain Pseudomonas sp. UW4 using molecular docking and molecular dynamics (MD) simulation. The absolute values of the lowest binding free energies of 18 out of the 59 compounds with the LBDs and the logarithm of the UW4 capillary chemotaxis threshold concentrations for the 18 compounds showed a negative correlation. The binding free energy of 1-aminocyclopropane-1-carboxylate (ACC) with the LBD of the corresponding chemoreceptor WP116 was the lowest among the 59 root exudate components and the 15 chemoreceptor LBDs analyzed. Knocking out wp116 significantly reduced the chemotaxis rate of UW4 to the wheat rhizosphere in the microcosm system. These results showed that molecular docking and MD simulation are efficient for analyzing the affinities between the root exudates and the chemoreceptor extracellular LBDs of PGPR for identifying the preferred chemoattractant of PGPR toward the rhizosphere, and ACC was determined to be the preferred chemoattractant for Pseudomonas sp. UW4 in colonizing the rhizosphere.