Pseudomonas syringae ve Pseudomonas savastanoi'deki mate ve IAAL proteinlerin in siliko karakterizasyonu

Three bacterial species from the Pseudomonas genus, Pseudomonas syringae pv. actinidiae, Pseudomonas syringae pv. tomato DC3000 and Pseudomonas savastanoi pv. savastanoi, are recognized as disease-causing agents. Recent analyses show a high correlation between both virulence and disease occurrence versus the expression of matE and iaaL genes and the corresponding MatE and IaaL proteins. These proteins are part of the Type 3 Secretion System bacterial machinery responsible for the delivery of the virulence factors of bacteria into the plant cell and are connected with the auxin hormone production, which in turn has a role in the plant disease. As MatE protein of Pseudomonas syringae pv. actinidiae is one of the main parts of the membrane transport machinery, its characterization helps us to determine the possible role of the protein in toxicity induction. We used different tools for the aforementioned analyzes. Using BLAST, we identified the full sequences of homologous MatE and IaaL proteins in all species containing them. Multiple sequence alignment helped us to identify the conservation level amongst proteins, polymorphisms, and similarities. The phylogenetic tree confirmed the MSA analysis results. Our protein of interest from three species has a positive phylogenetic distance from other species, and between each other. The 3D model of the MatE proteins from different species shows a tube-like structure made of alpha-helices interconnected by loops. The main differences between the studied proteins are the residue sequence in their loops. We found deletions and polymorphisms in the loop regions that may cause different folding patterns in the MatE proteins from the three species we analyzed, especially in the P. syringae pv. actinidiae. We found only one ligand, the "OLC" ligand interacting with MatE of P. syringae pv. actinidiae. It binds the inner part of the tube-like structure of MatE. According to STRING analysis, MatE interacts with only two other proteins, while IaaL has a wide network of interactions. All the MatE proteins have two MatE domains of the same size. The intergenic region of matE genes is highly conserved amongst the species. We found differences in the promoter regions. Polymorphisms in the promoter region might be one extra indicator of the particular characteristics of these proteins in Pseudomonas syringae pv. actinidiae and their influence on its toxicity in tomatoes and kiwi. Polymorphisms in the loop structures of MatE proteins and promoter regions might be the reason for the protein influence on the toxicity in the tomatoes and kiwi.