Genome Insight and factorial design to elucidate the regulation of the tryptophan-mediated IAA biosynthetic pathway in an endophyte

Endophytes are microorganisms that colonize plants, often via commensal or symbiotic associations, and regulate plant growth and metabolism. Such organisms are usually suitable alternatives to therapeuticallly relevant, bioactive, and commercially essential metabolites, particularly under optimized bioprocess conditions. The current study highlights the key research challenge of maximizing the production of Indole-3-Acetic Acid (IAA), a compound difficult to isolate from the plant due to low yield, by elucidating the genetic composition of an isolated endophyte and determining the biosynthetic pathway using the KEGG pathway. Moreover, deciphering the functional genomic and refining production optimization remain significant challenges. The whole-genome sequencing of the endophytic bacterium Bacillus cereus SKAM2 (Strain SKAM2) revealed a genome size of 5.6 Mb, a GC content of 36%, multiple tryptophan-dependent and tryptophan-independent pathways. Furthermore, the IAA biosynthetic pathways pave the way for process-optimization studies. The influence of various abiotic parameters and media supplements on IAA production in both intra- and extracellular media was compared, using a full-factorial design of experiments (DOE). The results showed the highest yield in the extracellular fraction, a 3.81-fold increase, exceeding the intracellular IAA yield. The results highlight the strong potential of strain SKAM2 as a microbial platform for sustainable IAA production.