Molecular basis of one-step methyl anthranilate biosynthesis in grapes, sweet orange, and maize.

Plants synthesize an array of volatile compounds, many of which serve ecological roles in attracting pollinators, deterring herbivores, and communicating with their surroundings. Methyl anthranilate (MeAA) is an anti-herbivory defensive volatile responsible for grape aroma that is emitted by several agriculturally relevant plants, including citrus, grapes, and maize. Unlike maize, which uses a one-step anthranilate methyltransferase (AAMT), grapes have been thought to use a two-step pathway for MeAA biosynthesis. By mining available transcriptomics data, we identified two AAMTs in Vitis vinifera (wine grape), as well as one ortholog in "Concord" grape. Many angiosperms methylate the plant hormone salicylic acid (SA) to produce methyl salicylate, which acts as a plant-to-plant communication molecule. Because the Citrus sinensis (sweet orange) SA methyltransferase can methylate both anthranilate (AA) and SA, we used this enzyme to examine the molecular basis of AA activity by introducing rational mutations, which identified several active site residues that increase activity with AA. Reversing this approach, we introduced mutations that imparted activity with SA in the maize AAMT, which uncovered different active site residues from those in the citrus enzyme. Sequence and phylogenetic analysis revealed that one of the Vitis AAMTs shares an ancestor with jasmonic acid methyltransferases, similar to the AAMT from strawberry (Frageria sp.). Collectively, these data demonstrate the molecular mechanisms underpinning AA activity across methyltransferases and identify one-step enzymes by which grapes synthesize MeAA.

Biochemical investigation of the tryptophan biosynthetic enzyme anthranilate phosphoribosyltransferase in plants.

While mammals require the essential amino acid tryptophan (Trp) in their diet, plants and microorganisms synthesize Trp de novo. The five-step Trp pathway starts with the shikimate pathway product, chorismate. Chorismate is converted to the aromatic compound anthranilate, which is then conjugated to a phosphoribosyl sugar in the second step by anthranilate phosphoribosyltransferase (PAT1). As a single-copy gene in plants, all fixed carbon flux to indole and Trp for protein synthesis, specialized metabolism, and auxin hormone biosynthesis proceeds through PAT1. While bacterial PAT1s have been studied extensively, plant PAT1s have escaped biochemical characterization. Using a structure model, we identified putative active site residues that were variable across plants and kinetically characterized six PAT1s (Arabidopsis thaliana (thale cress), Citrus sinensis (sweet orange), Pistacia vera (pistachio), Juglans regia (English walnut), Selaginella moellendorffii (spike moss), and Physcomitrium patens (spreading earth-moss)). We probed the catalytic efficiency, substrate promiscuity, and regulation of these six enzymes and found that the C. sinensis PAT1 is highly specific for its cognate substrate, anthranilate. Investigations of site-directed mutants of the A. thaliana PAT1 uncovered an active site residue that contributes to promiscuity. While Trp inhibits bacterial PAT1 enzymes, the six plant PAT1s that we tested were not modulated by Trp. Instead, the P. patens PAT1 was inhibited by tyrosine, and the S. moellendorffii PAT1 was inhibited by phenylalanine. This structure-informed biochemical examination identified variations in activity, efficiency, specificity, and enzyme-level regulation across PAT1s from evolutionarily diverse plants.

A structure-guided computational screening approach for predicting plant enzyme-metabolite interactions.

Plants are molecular factories that have spent millions of years evolving the enzymes needed to synthesize diverse primary and specialized metabolites. Despite the wealth of metabolites that plants produce, many of the enzymes responsible for generating these molecules have yet to be identified. For enzymes with known substrates, the extent of substrate promiscuity and small-molecule regulation remains unexplored. Many computational methods for identifying metabolic enzymes focus on gene-based approaches that rely on transcriptomics, metabolomics, and comparative genomics. With new AI-based tools for accurate protein structure prediction, protein-based strategies that screen a library of small molecules against a high-quality protein model can facilitate the identification of substrates, products, or inhibitors. Virtual screening has been used for structure-based drug design in the pharmaceutical industry for decades and easily translates to investigating plant metabolic enzymes. Here, we present a method for rapid, user-friendly, and open-source virtual screening using the Arabidopsis thaliana UGT74F2 with a curated library of specialized metabolites and herbicides and AutoDock Vina as an example. This method may be applied broadly to metabolic enzymes, and compound libraries can be easily adapted. Compounds are ranked based on their relative binding affinities and the resulting binding modes are evaluated using a molecular visualization program, like PyMOL. Because this is a computational approach, results from the virtual screen will need to be validated using in vitro or in vivo activity, binding, or inhibition assays. Virtual screening may aid in identifying substrates for enzymes of unknown function, revisiting substrate selectivity, or identifying natural or synthetic inhibitors.