Functional Prediction of <i>trans</i>-Prenyltransferases Reveals the Distribution of GFPPSs in Species beyond the Brassicaceae Clade
Terpenoids are the most diverse class of plant primary and specialized metabolites, and <i>trans</i>-prenyltransferases (<i>trans</i>-PTs) are the first branch point to synthesize precursors of various chain lengths for further metabolism. Whereas the catalytic mechanism of t...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-08-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/16/9471 |
| Summary: | Terpenoids are the most diverse class of plant primary and specialized metabolites, and <i>trans</i>-prenyltransferases (<i>trans</i>-PTs) are the first branch point to synthesize precursors of various chain lengths for further metabolism. Whereas the catalytic mechanism of the enzyme is known, there is no reliable method for precisely predicting the functions of <i>trans</i>-PTs. With the exponentially increasing number of available <i>trans</i>-PTs genes in public databases, an in silico functional prediction method for this gene family is urgently needed. Here, we present PTS-Pre, a web tool developed on the basis of the “three floors” model, which shows an overall 86% prediction accuracy for 141 experimentally determined <i>trans</i>-PTs. The method was further validated by in vitro enzyme assays for randomly selected <i>trans</i>-PTs. In addition, using this method, we identified nine new GFPPSs from different plants which are beyond the previously reported Brassicaceae clade, suggesting these genes may have occurred via convergent evolution and are more likely lineage-specific. The high accuracy of our blind prediction validated by enzymatic assays suggests that PTS-Pre provides a convenient and reliable method for genome-wide functional prediction of <i>trans</i>-PTs enzymes and will surely benefit the elucidation and metabolic engineering of terpenoid biosynthetic pathways. |
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| ISSN: | 1661-6596 1422-0067 |