Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

Abstract

Background: Taxus cells are a potential sustainable and environment-friendly source of taxol, but they have low survival ratios and slow grow rates. Despite these limitations, Taxus callus cells induced through 6 months of culture contain more taxol than their parent tissues. In this work, we utilized 6-month-old Taxus media calli to investigate their regulatory mechanisms of taxol biosynthesis by applying multiomics technologies. Our results provide insights into the adaptation strategies of T. media by transcriptional reprogramming when induced into calli from parent tissues.Results: Seven out of 12 known taxol, most of flavonoid and phenylpropanoid biosynthesis genes were significantly upregulated in callus cells relative to that in the parent tissue, thus indicating that secondary metabolism is significantly strengthened. The expression of genes involved in pathways metabolizing biological materials, such as amino acids and sugars, also dramatically increased because all nutrients are supplied from the medium. The expression level of 94.1% genes involved in photosynthesis significantly decreased. These results reveal that callus cells undergo transcriptional reprogramming and transition into heterotrophs. Interestingly, common defense and immune activities, such as "plant-pathogen interaction" and salicylic acid-and jasmonic acidsignaling transduction, were repressed in calli. Thus, it's an intelligent adaption strategy to use secondary metabolites as a cost-effective defense system. MiRNA-and degradome-sequencing results showed the involvement of a precise regulatory network in the miRNA-mediated transcriptional reprogramming of calli. MiRNAs act as direct regulators to enhance the metabolism of biological substances and repress defense activities. Given that only 17 genes of secondary metabolite biosynthesis were effectively regulated, miRNAs are likely to play intermediate roles in the biosynthesis of secondary metabolites by regulating transcriptional factors (TFs), such as ERF, WRKY, and SPL.

miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber (Cucumis sativus L.)

“…Further results suggest that increasing the biosynthesis of taxol and other secondary metabolites is an active regulatory measure of calli to adapt to the heterotrophic culture, and this alteration mainly involved direct and indirect miRNA-induced transcriptional reprogramming. These results expand the understanding of the relationships among the metabolism of biological substances, the biosynthesis of secondary metabolites and defense systems [22].…”

“…The miRNAs are by far the best characterized class of sRNAs. They are involved in a series of biological processes, such as growth and development [31,32], hormone signal transduction [22,33] and response to abiotic and biotic stresses [34,35].…”

Modification of Gene Expression, DNA Methylation and Small RNAs Expression in Rice Plants under In Vitro Culture

“…Tissue culture-induced somaclonal variations have long been observed, but genetic and the epigenetic changes associated with somaclonal variation are just beginning to be revealed in recent studies [40,[44][45][46]. In this study, we used stabilized regenerated lines and their WT donor of rice cv.…”

“…Misregulation of microRNAs and small RNA pathways can make a significant contribution to the phenomenon [31,49]. The miRNA pathway was unusually susceptible to tissue culture caused by potential alterations in both the microRNA and their target genes [44]. In addition, the 24-nt siRNAs are the inducer of RdDM and required for maintaining CHH methylation in plants [31].…”

“…miRNAs expression is affected by different stresses in plants which would regulate mRNA levels to respond to environmental alteration and affect plant development and growth [44,[51][52][53]. To clarify the targeted regulatory relationship between miRNAs and mRNAs, single miRNA to mRNA analysis or miRNA-mRNA integrated analysis are widely conducted [54,55].…”