Abstract Detail

Comparative Genomics/Transcriptomics

Auber, Robert [1], Crook, Joseph [2], Widhalm, Joshua [2], Wisecaver, Jennifer [1].

Identifying Gene Candidates of the Shikonin Biosynthesis Pathway in the Chinese Medicinal Plant Lithospermum erythrorhizon.

Specialized metabolites (SMs) are products of metabolism that are not directly involved in growth or development but aid in the survival of the producer. As such, SMs display a variety of ecologically important  properties such as antibiotic activity or color pigmentation, which also makes SMs of high interest for their medicinal and biotechnological applications. SM compounds are intricate and assembled by biological pathways that can be equally complex. Due to the high level of evolutionary divergence seen in these pathways, characterizing the genes responsible for SM production can pose a significant challenge. One SM, shikonin, is produced by the Chinese medicinal plant Lithospermum erythrorhizon. Shikonin is known for its use in dyes, cosmetics and in traditional medicine, and has more recently been demonstrated to exhibit antiviral and anticancer activities. Only one enzymatic gene has been elucidated in this SM pathway: PGT, which encodes a prenyltransferase involved in the committing step of shikonin synthesis from 4-hydroxybenzoic acid (4HBA). In this study, we performed a differential expression analysis to construct a list of gene candidates potentially involved in shikonin biosynthesis. Leveraging the exclusivity of shikonin production in the root periderm, we compared gene expression between periderm and vascular regions of L. erythrorhizon root as well as whole root and leaf tissue. We identified a 56-gene module, which contained the known shikonin gene PGT. This module was highly expressed in root periderm and lowly expressed in leaves and root vascular tissue. GO enrichment analysis suggests this module may function in hydroquinone oxygen oxidoreductase activity and NAD(P)H dehydrogenase quinone activity, which is in agreement with the proposed biosynthetic pathway of shikonin.  In future work, we will perform additional RNAseq experiments taking advantage of other conditions known to modulate shikonin production to refine our list of candidates. Lastly, the gene candidates obtained in this study will be functionally tested by molecular cloning in L. erythrorhizon hairy root cultures.

1 - Purdue University, 175 South University street, West Lafayette, IN, 47907, United States
2 - Purdue University, 625 Agriculture Mall drive, West Lafayette, IN, 47907, United States

Specialized Metabolite
De novo Transcriptome
Differential Expression Analysis.

Presentation Type: Poster
Number: PGT006
Abstract ID:142
Candidate for Awards:Genetics Section Poster Award

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