Does metabolic pathway dissection need whole genome sequences of plants?
It is time-consuming and laborious to explore the biosynthetic pathway of non-metabolic gene clusters. We proposed an effective methodology to dissect the complex biosynthetic pathway in medicine plant with a giant genome, which did not contain related metabolic gene cluster. The candidates include several CYPs identified in previous research and one UGT characterized in this study, which fully prove the effectiveness of this method. This study provides a new idea for the study of gene cluster deficiency biosynthesis pathways in medicinal plants.
Plants are rich in a variety of metabolites with diverse bioactivities, whose contents are extremely low in plant tissues. Studies on the biosynthetic pathways of these metabolites are very important for producing them using heterologous expression system. Scientists mainly use multi-omics methods to analyze the biological pathways of metabolites. Although genomic and transcriptional information of numerous medicine plants have been generated and made available to public, the progress of candidate gene mining and whole pathway dissection of specialized plant metabolites remains slow due to the following factors1, 2, 3, 4, 5. The biosynthesis of several specified metabolites lacks tissue specificity, which hinders the prediction of the metabolic biosynthetic genes by simple differentially expression analysis6. The divergent evolution of metabolic gene families generated numerous individual members that are phylogenetically close and can decorate diverse type of natural products. For this reason, predicting the related pathway gene solely based on phylogenetic analysis is impossible7. In addition, the biosynthetic genes of specific plant metabolites are scattered in different regions of the genome, further increasing the difficulty in identifying candidates precisely by physical distance of metabolic pathway-related genes8, 9, even if the generation and good assembly of whole-genome sequences10, 11. Therefore, an efficient strategy needs to be developed and improved urgently to accurately predict the key genes in the complex none-clustered biosynthetic pathway of specialized plant metabolites.
The co-expression network analysis combining the distributions of specific metabolites, different gene expressions, and phylogenetic analysis was used to predict the key genes involved in the biosynthetic pathway of steroidal saponins in P. polyphylla, a medicine plant with more 50 Gb genome size. This study provides a universal method to elucidate the complex pathway of other specialized plant metabolites.
- Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annual review of genomics and human genetics 10, 135-151 (2009).
- Yin Y, Gao L, Zhang X, Gao W. A cytochrome P450 monooxygenase responsible for the C-22 hydroxylation step in the Paris polyphylla steroidal saponin biosynthesis pathway. Phytochemistry 156, 116-123 (2018).
- Liu T, Li X, Xie S, Wang L, Yang S. RNA-seq analysis of Paris polyphylla var. yunnanensis roots identified candidate genes for saponin synthesis. Plant diversity 38, 163-170 (2016).
- Yang Z, et al. Transcriptome analyses of Paris polyphylla var. chinensis, Ypsilandra thibetica, and Polygonatum kingianum characterize their steroidal saponin biosynthesis pathway. Fitoterapia 135, 52-63 (2019).
- Christ B, et al. Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants. Nature communications 10, 3206 (2019).
- Han JY, In JG, Kwon YS, Choi YE. Regulation of ginsenoside and phytosterol biosynthesis by RNA interferences of squalene epoxidase gene in Panax ginseng. Phytochemistry 71, 36-46 (2010).
- Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. The Plant journal : for cell and molecular biology 90, 764-787 (2017).
- Mylona P, et al. Sad3 and sad4 are required for saponin biosynthesis and root development in oat. Plant Cell 20, 201-212 (2008).
- Shang Y, et al. Plant science. Biosynthesis, regulation, and domestication of bitterness in cucumber. Science 346, 1084-1088 (2014).
Journal: Communications Biology.
DOI : 10.1038/s42003-022-03000-z
Title : Effective prediction of biosynthetic pathway genes involved in bioactive polyphyllins in Paris polyphylla .