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Terzyme: a tool for identification and analysis of the plant terpenome

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Title Terzyme: a tool for identification and analysis of the plant terpenome
 
Creator Priya, Piyush
Yadav, Archana
Chand, Jyoti
Yadav, Gitanjali
 
Subject Terpenome
Terpene synthase (TPS)
Prenyl transferase (PT)
Hidden Markov Models (HMM)
GO clustering
Pathway mapping
Phytochemicals
 
Description Accepted date: 19 December 2017
BACKGROUND:
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'. 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.

RESULTS:
We 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.

CONCLUSIONS:
Terzyme 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.
This work was supported by the BTISNET-grant of Department of Biotechnology (DBT), Govt of India (Grant No. BT/BI/04/069/2006), and the SERB Women’s Excellence Award to GY (Grant No. SB/WEA-014/2013). PP was supported by Senior Research Fellowship (SRF) of the Council of Scientific and Industrial Research (CSIR), India. J is supported by the BTISNET grant mentioned above. AY is supported by Senior Research Fellowship (SRF) of University Grants Commission.
 
Date 2018-01-23T04:38:58Z
2018-01-23T04:38:58Z
2018
 
Type Article
 
Identifier Plant Methods, 14: 4
1746-4811
http://223.31.159.10:8080/jspui/handle/123456789/826
https://plantmethods.biomedcentral.com/articles/10.1186/s13007-017-0269-0
10.1186/s13007-017-0269-0
 
Language en_US
 
Format application/pdf
 
Publisher BioMed Central Ltd