Bioinformatics Analysis of the Two-Component Signal Transduction System NtrYX in Cereibacter azotoformans

Abstract

Cereibacter azotoformans is a facultative anaerobic bacterium with important nitrogen fixation ability, and its NtrYX two-component signal transduction system plays a key role in regulating nitrogenase activity. The NtrYX two-component signal transduction system is an important regulatory mechanism within bacteria. The system perceives and responds to environmental signals through the interaction between HK (histidine kinase) and RR (response regulatory protein). However, there is currently a lack of research on the structure and function of the C. azotoformans NtrYX two-component system in China. This study used bioinformatics methods to deeply analyze the structure and function of the C. azotoformans NtrYX system in China. Through sequence retrieval and domain analysis, we identified the key structural domains and their functions of NtrY and NtrX proteins, NtrY includes HAMP PAS, PAC, HisKA, HATPase_c, NtrX includes REC and AAA domains. The COACH tool was used to predict potential signal molecules in the extracellular signal sensing region of NtrY, and the interaction between the active region of NtrY's extracellular signal sensing region and small molecules was analyzed using and LigPlot+. Among them, Arg215 and Arg198 have strong hydrogen bonding interactions with small molecules. The molecular docking between NtrY and ATP indicates that the stimulation of external signals strengthens the alpha helix interaction of the HisKA domain, making it active and hydrogen bonding stronger, leading to changes in the HisKA structure and providing spatial distance for phosphorylation. By using the COACH server to predict the interaction between NtrX and ADP, it was found that the residue Ser173 Gly174, Val354, and Arg355 have strong hydrogen bonding interactions with ADP. In addition, the simulated interaction between NtrY and NtrX proteins indicates that, the binding between the PAS region and the REC region is crucial for the signal transduction chain. This study analyzed the structural information of each key link in the NtrYX two-component signal transduction system using bioinformatics methods, and preliminarily revealed the NtrYX two-component signal transduction mechanism. The conclusion of the study provides theoretical support for protein engineering modification to improve the signal response level of the NtrYX two-component system, laying a foundation for further research on the mechanism of the C. azotoformans NtrYX two-component system.