Abstract:[Objective] Indole-3-acetic acid is crucial for plant growth and development and physiological activities. Indole-3-acetic acid N-acetyltransferase YsnE plays an important part in indole-3-acetic acid synthesis. This study aims to analyze the metabolic pathways of YsnE involved in indole-3-acetic acid synthesis of Bacillus amyloliquefaciens. [Methods] Through deletion and overexpression of ysnE, the role of ysnE in indole-3-acetic acid synthesis was elucidated. Combined with the addition of indole-3-acetic acid synthesis intermediates (indole pyruvic acid (IPA), indole-3-acetamide (IAM), tryptamine (TAM), indole-3-acetonitrile (IAN)) and in vitro enzymatic conversion experiments, the metabolic pathways of ysnE involved in indole-3-acetic acid synthesis were clarified. [Results] YsnE played an important role in indole-3-acetic acid synthesis in B. amyloliquefaciens HZ-12. The amount of IPA, IAM, and IAN consumed in ysnE deletion strain was significantly reduced, and YsnE functioned as indolepyruvate decarboxylase YclB, and indoleacetamide hydrolase/nitrilase/nitrile hydratase YhcX, and affected indole-3-acetic acid synthesis by participating in IPA, IAM, and IAN pathways. [Conclusion] YsnE influences the IPA, IAM, and IAN pathways to involve in indole-3-acetic acid synthesis, which lays a foundation for analysis of indole-3-acetic acid synthesis pathway and breeding strains with high yield of indole-3-acetic acid by metabolic engineering.