Indole-3-Acetic Acid Production and Molecular Insights into its Biosynthetic Pathway

IAA synthesis by endophytes plays an important role in establishing a successful relationship between bacteria and plants. There are multiple pathways of IAA biosynthesis, IPyA pathway being widespread among endophytes. A total of five bacterial endophytes, Pseudomonas lini PRN1, Bacillus sp. PHR5, Ochrobactrum sp. PHR6, Bacillus sp. AJhN4 and Pantoea agglomerans CPHN2, were used in the present study. Out of these, three isolates Bacillus sp. PHR5, Ochrobactrum sp. PHR6, and Bacillus sp. AJhN4 were screened and optimized for IAA production by varying physicochemical parameters using OFAT. The presence of IAA in crude extracts was confirmed by ultra-performance liquid chromatography (UPLC) using IAA as standard. The highest IAA producing isolate was further used for scale-up of IAA production. Maximum production of 947 µg/ml IAA was obtained with 10% inoculum size, pH 9, DO of 60 after 19 h at 30 °C using 2-L stirred tank bioreactor. The study was further carried out, to specifically decipher the IAA pathway in this isolates and to characterize the ipdC gene. The genomic analysis of ipdC gene sequence of P. agglomerans CPHN2 performed and specific primers designed after annotation and amplicons of size 1720 bp and 2500 bp were obtained respectively. It was also observed that the IPDC protein is coded by the negative or antisense strand of DNA. Homology modelling approach was employed to develop a structural model of the IPDC proteins by utilizing sequences from closely related organisms, as well as from P. agglomerans CPHN2 IPDC protein sequence. All IPDC protein models exhibited significantly higher binding energy with indole-3-pyruvate compared to pyruvate. Among these, the IPDC from P. agglomerans CPHN2 showed the maximum binding energy with indole-3-pyruvate relative to other IPDC proteins. In the present study, the identification of the Indole-3-pyruvate (IPyA) pathway and characterization of the ipdC gene in Pantoea agglomerans offers insights into optimizing the IAA production for sustainable agriculture. Understanding the enzymatic pathways also opens avenues for genetic engineering in microbial biotechnology.

The online version contains supplementary material available at 10.1007/s12088-025-01535-3.