Cutting-edge plant natural product pathway elucidation

Abstract

Plant natural products (PNPs) play important roles in plant physiology and have been applied across diverse fields of human society. Understanding their biosynthetic pathways informs plant evolution and meanwhile enables sustainable production through metabolic engineering. However, the discovery of PNP biosynthetic pathways remains challenging due to the diversity of enzymes involved and limitations in traditional gene mining approaches. In this review, we will summarize state-of-the-art strategies and recent examples for predicting and characterizing PNP biosynthetic pathways, respectively, with multiomics-guided tools and heterologous host systems and share our perspectives on the systematic pipelines integrating these various bioinformatic and biochemical approaches.

Figure 1.. Overview of PNP biosynthetic pathway discovery challenges and elucidation methods.

A) An abstract PNP biosynthetic pathway depicts the challenges associated with PNP pathway discovery, which are largely related to the complexity of these pathways. This includes many cascading steps between substrates (S) and intermediates (I), which may require elicitation by a stimulus and may be localized across different plant tissues or subcellular compartments, such as the chloroplast or vacuole. B) Tools for PNP pathway prediction include genomic, transcriptomic, proteomic, interactomic, and metabolomic analysis methods. These methods are frequently used in combination to allow for analysis of the correlated spatial and/or temporal presence of various pathway-associated molecules. C) Once genes predicted to be involved in PNP biosynthesis have been identified, they can be functionally characterized in heterologous host systems (e.g. model plants such as Nicotiana benthamiana or microbes such as Escherichia coli or Saccharomyces cerevisiae), in vitro, or through gene silencing in the native host plant. Created with BioRender.com.