Effective prediction of biosynthetic pathway genes involved in bioactive polyphyllins in Paris polyphylla

Xin Hua,Zheyong Xue,Baozhong Duan,Zhichao Xu,Kangzong Wang,Changqi Hao,Xue Yin,Wei Song,Tongbing Su

doi:10.1038/s42003-022-03000-z

Abstract

The genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network in Paris polyphylla with a giant genome. The lack of genomic data and tissue specificity causes the study of the biosynthetic pathway notably difficult. Here, we report an effective method for the prediction of key genes of polyphyllin biosynthesis. Full-length transcriptome from eight different organs via hybrid sequencing of next generation sequencingand third generation sequencing platforms annotated two 2,3-oxidosqualene cyclases (OSCs), 216 cytochrome P450s (CYPs), and 199 UDP glycosyltransferases (UGTs). Combining metabolic differences, gene-weighted co-expression network analysis, and phylogenetic trees, the candidate ranges of OSC, CYP, and UGT genes were further narrowed down to 2, 15, and 24, respectively. Beside the three previously characterized CYPs, we identified the OSC involved in the synthesis of cycloartenol and the UGT (PpUGT73CR1) at the C-3 position of diosgenin and pennogenin in P. polyphylla. This study provides an idea for the investigation of gene cluster deficiency biosynthesis pathways in medicinal plants.

Highlights

The genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network in Paris polyphylla with a giant genome
The biosynthetic pathway of polyphyllins begins with the condensation of two molecules of isopentenyl diphosphate and one molecule of dimethylallyl diphosphate, which is catalyzed by farnesyl diphosphate synthase (FPS) to form farnesyl diphosphate (FPP, C15)[9]
FPP molecules are catalyzed by squalene synthase (SQS) to produce a linear C30 molecule, squalene, which is further cycled by squalene epoxidase to 2,3-oxidosqualene[9]

Summary

Introduction

The genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network in Paris polyphylla with a giant genome. Beside the three previously characterized CYPs, we identified the OSC involved in the synthesis of cycloartenol and the UGT (PpUGT73CR1) at the C-3 position of diosgenin and pennogenin in P. polyphylla. The rhizome of this plant is an important component of the traditional Chinese medicines “Yunnan Baiyao” and “Gongxue Ning”[1], which have pharmacological activities, such as hemostasis, analgesic, sedation, anti-inflammatory, and antitumor effects[2,3,4]. The biosynthetic pathway of polyphyllins begins with the condensation of two molecules of isopentenyl diphosphate and one molecule of dimethylallyl diphosphate, which is catalyzed by farnesyl diphosphate synthase (FPS) to form farnesyl diphosphate (FPP, C15)[9]. Enzymes in the CYP90G family can catalyze the hydroxylation of cholesterol C-16 and

Methods

Results

Conclusion