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Comparative Transcriptome Profiles of Human HaCaT Cells in Response to Gynostemma pentaphyllum Extracts Obtained Using Three Independent Methods by RNA Sequencing.

ABSTRACT: Gynostemma pentaphyllum (GP) is widely used in herbal medicine. In this study, we developed a method for the large-scale production of GP cells using plant tissue culture techniques combined with bioreactors. Six metabolites (uridine, adenosine, guanosine, tyrosine, phenylalanine, and tryptophan) were identified in GP extracts. Transcriptome analyses of HaCaT cells treated with GP extracts using three independent methods were conducted. Most differentially expressed genes (DEGs) from the GP-all condition (combination of three GP extracts) showed similar gene expression on treatment with the three individual GP extracts. The most significantly upregulated gene was LTBP1. Additionally, 125 and 51 genes were upregulated and downregulated, respectively, in response to the GP extracts. The upregulated genes were associated with the response to growth factors and heart development. Some of these genes encode components of elastic fibers and the extracellular matrix and are associated with many cancers. Genes related to folate biosynthesis and vitamin D metabolism were also upregulated. In contrast, many downregulated genes were associated with cell adhesion. Moreover, many DEGs were targeted to the synaptic and neuronal projections. Our study has revealed the functional mechanisms of GP extracts' anti-aging and photoprotective effects on the skin using RNA sequencing.

SUBMITTER: Cho WK

PROVIDER: S-EPMC9961609 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Comparative Transcriptome Profiles of Human HaCaT Cells in Response to <i>Gynostemma pentaphyllum</i> Extracts Obtained Using Three Independent Methods by RNA Sequencing.

Cho Won Kyong WK Paek Seung Hye SH Kim Soo-Yun SY Jang Sung Joo SJ Lee Sak S Choi Hoseong H Jo Yeonhwa Y Lee Jeong Hun JH Moh Sang Hyun SH

Life (Basel, Switzerland) 20230202 2

<i>Gynostemma pentaphyllum</i> (GP) is widely used in herbal medicine. In this study, we developed a method for the large-scale production of GP cells using plant tissue culture techniques combined with bioreactors. Six metabolites (uridine, adenosine, guanosine, tyrosine, phenylalanine, and tryptophan) were identified in GP extracts. Transcriptome analyses of HaCaT cells treated with GP extracts using three independent methods were conducted. Most differentially expressed genes (DEGs) from the ...[more]

PMID: 36836780

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Project description:BackgroundGypenosides are a group of triterpene saponins from Gynostemma pentaphyllum that are the same as or very similar to ginsenosides from the Panax species. Several enzymes involved in ginsenoside biosynthesis have been characterized, which provide important clues for elucidating the gypenoside biosynthetic pathway. We suppose that gypenosides and ginsenosides may have a similar biosynthetic mechanism and that the corresponding enzymes in the two pathways may have considerable similarity in their sequences. To further understand gypenoside biosynthesis, we sequenced the G. pentaphyllum transcriptome with a hybrid sequencing-based strategy and then determined the candidate genes involved in this pathway using phylogenetic tree construction and gene expression analysis.ResultsFollowing the PacBio standard analysis pipeline, 66,046 polished consensus sequences were obtained, while Illumina data were assembled into 140,601 unigenes with Trinity software. Then, these output sequences from the two analytical routes were merged. After removing redundant data with CD-HIT software, a total of 140,157 final unigenes were obtained. After functional annotation, five 2,3-oxidosqualene cyclase genes, 145 cytochrome P450 genes and 254 UDP-glycosyltransferase genes were selected for the screening of genes involved in gypenoside biosynthesis. Using phylogenetic analysis, several genes were divided into the same subfamilies or closely related evolutionary branches with characterized enzymes involved in ginsenoside biosynthesis. Using real-time PCR technology, their expression patterns were investigated in different tissues and at different times after methyl jasmonate induction. Since the genes in the same biosynthetic pathway are generally coexpressed, we speculated that GpOSC1, GpCYP89, and GpUGT35 were the leading candidates for gypenoside biosynthesis. In addition, six GpWRKYs and one GpbHLH might play a possible role in regulating gypenoside biosynthesis.ConclusionsWe developed a hybrid sequencing strategy to obtain longer length transcriptomes with increased accuracy, which will greatly contribute to downstream gene screening and characterization, thus improving our ability to elucidate secondary metabolite biosynthetic pathways. With this strategy, we found several candidate genes that may be involved in gypenoside biosynthesis, which laid an important foundation for the elucidation of this biosynthetic pathway, thus greatly contributing to further research in metabolic regulation, synthetic biology and molecular breeding in this species.

Dataset Information

Comparative Transcriptome Profiles of Human HaCaT Cells in Response to Gynostemma pentaphyllum Extracts Obtained Using Three Independent Methods by RNA Sequencing.

Publications

Comparative Transcriptome Profiles of Human HaCaT Cells in Response to <i>Gynostemma pentaphyllum</i> Extracts Obtained Using Three Independent Methods by RNA Sequencing.

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