Abstract
BackgroundTerpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its ‘terpenome’. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data.ResultsWe have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants.ConclusionsTerzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes.
Highlights
Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its ‘terpenome’
Biosynthesis of terpenes requires the condensation of universal precursor C 5 isoprene units to form C15 or C20 prenyl diphosphates (PDPs), catalyzed by short chain prenyl transferase (PT) enzymes, followed by multi-step cyclization reactions catalysed by a huge family of unique enzymes called the terpene synthases (TPSs) [5, 6]
We present a comprehensive attempt to identify and classify the PT and TPS gene families in 42 plant species for which nuclear genome sequence data is available in the public domain, leading to the development of Terzyme, an interactive online webserver and database for predictive identification and analysis of the plant terpenome
Summary
Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its ‘terpenome’. Modern plants have adapted to the sessile nature of life on land by evolving mechanisms for chemical communication and defence, mediated via low molecular weight compounds, often with complex structures, which have the ability to function in diverse physiological, developmental and evolutionary processes [1] These phytochemicals, grouped together as plant secondary metabolites, have diversified in both structure and function via gene duplications followed by sub-functionalisation and positive selection for metabolite expansion, such that each. Priya et al Plant Methods (2018) 14:4 can be made from a single substrate by binding and steering polyisoprene substrates through a precise, multistep cyclization cascade that is initiated by the propagation of a highly reactive carbocation [7, 8] Both PTs and TPSs have a distinct ‘terpene fold’ composed largely of inert amino acids (aa) lining a central active site [9]. TPSs have been identified and characterized in model plant species of commercial and agronomic value such as Arabidopsis thaliana [12], Citrus [13], Vitis vinifera [14] and Solanum lycopersicum [15], as well as in various gymnosperms [16,17,18]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
