Biology subjects

Pichersky, E.

Publications and source records attributed to Pichersky, E..

3 recordsLinked to original sources

bioRxiv2026

An early-diverging Caladeniinae orchid reveals diversification of terpene and apocarotenoid pathways underlying floral scent evolution

Orchids exhibit extraordinary floral diversity, yet the molecular mechanisms underlying floral scent evolution remain poorly understood. Guided by recent phylogenomic reconstruction of the Australian orchid subtribe Caladeniinae, we used Glossodia major, an earlier-diverging food-deceptive lineage, as an evolutionary anchor for investigating floral volatile diversification. Scent-producing petals showed coordinated expression of terpene synthase (TPS), carotenoid and carotenoid cleavage dioxygenase (CCD) pathways. Functional characterisation identified GmTPS-b3, GmTPS-b4 and GmTPS-a1 as contributors to floral monoterpene and sesquiterpene production, while GmCCD1 produced geranylacetone, the dominant floral volatile, from {zeta}-carotene. GmCCD4 and GmCCD7a showed additional, partially overlapping apocarotenoid-forming activities. Integration of tissue-specific expression, enzyme activity and subcellular localisation linked these pathways to the emitted floral bouquet. Functional comparisons with characterised Caladenia homologues revealed biochemical conservation and catalytic and compartmental specialisation, while expression profiling across 31 species identified pollination strategy-associated regulatory divergence in TPSa1 and TPSb3, consistent with corresponding shifts in terpenoid-rich floral scent. We propose that differential modification and deployment of conserved biosynthetic pathways contributed to the attenuation and re-emergence of terpenoid-rich floral scent during Caladeniinae diversification. More broadly, our findings provide candidate mechanistic links between molecular evolution, pollinator-mediated selection and floral diversification.

plant biology↗

bioRxiv2021

Synthesis of 4-methylvaleric acid, a precursor of pogostone, involves a 2-isobutylmalate synthase related to 2-isopropylmalate synthase of leucine biosynthesis

O_LIWe show here that the side chain of pogostone, one of the major components of patchouli oil obtained from Pogostemon cablin and possessing a variety of pharmacological activities, is derived from 4-methylvaleric acid. C_LIO_LIWe also show that 4-methylvaleric acid is produced through the one-carbon - ketoacid elongation pathway with the involvement of the key enzyme 2- isobutylmalate synthase (IBMS), a newly identified enzyme related to isopropylmalate synthase (IPMS) of Leu biosynthesis. C_LIO_LISite-directed mutagenesis identified Met132 in the N-terminal catalytic region as affecting the substrate specificity of PcIBMS1. And even though PcIBMS1 possesses the C-terminal domain that in IPMS serves to mediate Leu inhibition, it is insensitive to Leu. C_LIO_LIThe observation of the evolution of IBMS from IPMS, as well as previously reported examples of IPMS-related genes involved in making glucosinolates in Brassicaceae, acylsugars in Solanaceae, and flavor compounds in apple, indicate that IPMS genes represent an important pool for the independent evolution of genes for specialized metabolism. C_LI One Sentence SummaryWe describe a novel enzyme, 2-isobutylmalate synthase, that is related to 2-isopropylmalate synthase and is able to efficiently convert 4-methyl-2- oxovalerate to 2-isobutylmalate, a key intermediate in the synthesis of the pogostone precursor 4-methylvaleric acid.

plant biology↗

bioRxiv2018

Robust predictions of specialized metabolism genes through machine learning

Plant specialized metabolism (SM) enzymes produce lineage-specific metabolites with important ecological, evolutionary, and biotechnological implications. Using Arabidopsis thaliana as a model, we identified distinguishing characteristics of SM and GM (general metabolism, traditionally referred to as primary metabolism) genes through a detailed study of features including duplication pattern, sequence conservation, transcription, protein domain content, and gene network properties. Analysis of multiple sets of benchmark genes revealed that SM genes tend to be tandemly duplicated, co-expressed with their paralogs, narrowly expressed at lower levels, less conserved, and less well connected in gene networks relative to GM genes. Although the values of each of these features significantly differed between SM and GM genes, any single feature was ineffective at predicting SM from GM genes. Using machine learning methods to integrate all features, a well performing prediction model was established with a true positive rate of 0.87 and a true negative rate of 0.71. In addition, 86% of known SM genes not used to create the machine learning model were predicted as SM genes, further demonstrating its accuracy. We also demonstrated that the model could be further improved when we distinguished between SM, GM, and junction genes responsible for reactions shared by SM and GM pathways. Application of the prediction model led to the identification of 1,217 A. thaliana genes with previously unknown functions, providing a global, high-confidence estimate of SM gene content in a plant genome.\n\nSignificanceSpecialized metabolites are critical for plant-environment interactions, e.g., attracting pollinators or defending against herbivores, and are important sources of plant-based pharmaceuticals. However, it is unclear what proportion of enzyme-encoding genes play roles in specialized metabolism (SM) as opposed to general metabolism (GM) in any plant species. This is because of the diversity of specialized metabolites and the considerable number of incompletely characterized pathways responsible for their production. In addition, SM gene ancestors frequently played roles in GM. We evaluate features distinguishing SM and GM genes and build a computational model that accurately predicts SM genes. Our predictions provide candidates for experimental studies, and our modeling approach can be applied to other species that produce medicinally or industrially useful compounds.

plant biology↗