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Domingues DS, Oliveira LS, Lemos SMC, Barros GCC, Ivamoto-Suzuki ST. A Bioinformatics Tool for Efficient Retrieval of High-Confidence Terpene Synthases (TPS) and Application to the Identification of TPS in Coffea and Quillaja. Methods Mol Biol 2022; 2469:43-53. [PMID: 35508828 DOI: 10.1007/978-1-0716-2185-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Terpenoids are a class of compounds that are found in all living organisms. In plants, some terpenoids are part of primary metabolism, but most terpenes found in plants are classified as specialized metabolites, encoded by terpene synthases (TPS). It is not obvious how to assign the putative product of a given TPS using bioinformatics tools. Phylogenetic analyses easily assign TPS into families; however members of the same TPS family can synthetize more than one terpenoid-and, in many biotechnological applications, researchers are more interested in the product of a given TPS rather than its phylogenetic profile. Automated protein annotation can be used to classify TPS based on their products, despite the family they belong to. Here, we implement an automated bioinformatics method, search_TPS, to identify TPS proteins that synthesize mono, sesqui and diterpenes in Angiosperms. We verified the applicability of the method by classifying wet lab validated TPS and applying it to find TPS proteins in Coffea arabica, C. canephora, C. eugenioides, and Quillaja saponaria. Search_TPS is a computational tool based on PERL scripts that carries out a series of HMMER searches against a curated database of TPS profile hidden Markov models. The tool is freely available at https://github.com/liliane-sntn/TPS .
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Affiliation(s)
- Douglas S Domingues
- Group of Genomics and Transcriptomes in Plants, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil.
- Graduate Program in Bioinformatics, Federal University of Technology - Paraná, UTFPR, Cornélio Procópio, Brazil.
- Graduate Program in Genetics, Institute of Biosciences, São Paulo State University, UNESP, Botucatu, Brazil.
- Graduate Program in Plant Biology, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil.
| | - Liliane S Oliveira
- Graduate Program in Bioinformatics, Federal University of Technology - Paraná, UTFPR, Cornélio Procópio, Brazil.
| | - Samara M C Lemos
- Group of Genomics and Transcriptomes in Plants, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
- Graduate Program in Genetics, Institute of Biosciences, São Paulo State University, UNESP, Botucatu, Brazil
| | - Gian C C Barros
- Group of Genomics and Transcriptomes in Plants, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
- Graduate Program in Plant Biology, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Suzana T Ivamoto-Suzuki
- Group of Genomics and Transcriptomes in Plants, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil.
- Department of Agronomy, State University of Londrina, UEL, Londrina, Brazil.
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