Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways

Integration of CRISPR/Cas9 with multi-omics technologies to engineer secondary metabolite productions in medicinal plant: Challenges and Prospects

Plants acts as living chemical factories that may create a large variety of secondary metabolites, most of which are used in pharmaceutical products. The production of these secondary metabolites is often much lower. Moreover, the primary constraint after discovering potential metabolites is the capacity to manufacture sufficiently for use in industrial and therapeutic contexts. The development of omics technology has brought revolutionary discoveries in various scientific fields, including transcriptomics, metabolomics, and genome sequencing. The metabolic pathways leading to the utilization of new secondary metabolites in the pharmaceutical industry can be identified with the use of these technologies. Genome editing (GEd) is a versatile technology primarily used for site-directed DNA insertions, deletions, replacements, base editing, and activation/repression at the targeted locus. Utilizing GEd techniques such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9), metabolic pathways engineered to synthesize bioactive metabolites optimally. This article will briefly discuss omics and CRISPR/Cas9-based methods to improve secondary metabolite production in medicinal plants.

Integrated genomic, transcriptomic, and metabolomic analyses of Ilex hylonoma provide insights into the triterpenoid saponin biosynthesis

Ilex is known for its rich content of secondary metabolites, particularly triterpenoid saponins. These compounds hold significant value in natural remedies and herbal medicine. However, the molecular mechanisms responsible for triterpenoid biosynthesis in plants of this genus remain largely unexplored. In this study, we successfully generated the first chromosome-scale genome of Ilex hylonoma. The assembly, comprising 20 anchored chromosomes, has an N50 contig size of 2.13 Mb and a scaffold size of 33.68 Mb. Comparative genome analyses with two other congeners with available chromosome-level genomes suggested that an end-to-end chromosome fusion event likely contributed to the reduction in chromosome number from n = 20 to n = 19 within this genus. By integrating transcriptomic and metabolomic data, we identified the gene expression patterns and metabolite profiles of I. hylonoma across three commonly utilized medicinal tissues. We subsequently pinpointed candidate genes involved in the regulation of triterpenoid saponin biosynthesis, including CYP450 genes, UGT genes, and associated transcription factors. Furthermore, yeast heterologous expression analysis revealed that ihyl08363 catalyzed the conversion of β-amyrin into oleanolic acid, while ihyl04303 catalyzed the C-2α hydroxylation of oleanolic acid to produce maslinic acid. This integrated analysis provides valuable insights into the biosynthesis of important triterpenoid saponins in medicinal Ilex plants.

Metabolite profiling reveals the influence of grapevine genetic distance on the chemical signature of juices

BACKGROUND

Yield, disease tolerance, and climate adaptation are important traits in grapevine genetic breeding programs. Selection for these characteristics causes unpredictable changes in primary and specialized metabolism, affecting the physicochemical properties and chemical composition of the berries and their processed products, juice, and wine. In this study, we investigated the influence of the genetic distance between grapevine genotypes on the chemical signatures of the juices, by integrating comprehensive metabolic profiling to genetic analyses.

RESULTS

The studied grapevine cultivars exhibited low genetic diversity. Breeding for agronomic traits promoted higher contents of soluble sugars, total phenolics, and anthocyanins in the juices. Untargeted juice metabolomics identified a total of 147 metabolites, consisting of 30 volatiles, 21 phenolics, and 96 ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) features. Juices from grapes of the most recent cultivars exhibited increased levels of trans-resveratrol, catechin, and luteolin. The blend of volatiles from juices of later cultivars was also more complex, consisting of 29 distinct metabolites in 'BRS Magna'. Grapes from 'BRS Carmem', an intermediate cultivar, gave the most divergent UHPLC-MS juice profile.

CONCLUSION

Contents of soluble solids, total phenolics, and anthocyanins in grape juices were increased by controlled crosses and hybrid selection. Integrative analyses demonstrated that the juices' metabolic profiles accurately represent the cultivars' genetic distances. Juices from 'BRS Violeta' and 'BRS Magna' show relevant positive association with health-related phenolics and a distinct set of odor volatiles, although these characteristics were specifically sought by breeding. © 2023 Society of Chemical Industry.

Deoxynivalenol accumulation and detoxification in cereals and its potential role in wheat-Fusarium graminearum interactions

Deoxynivalenol (DON) is a prominent mycotoxin showing significant accumulation in cereal plants during infection by the phytopathogen Fusarium graminearum. It is a virulence factor that is important in the spread of F. graminearum within cereal heads, and it causes serious yield losses and significant contamination of cereal grains. In recent decades, genetic and genomic studies have facilitated the characterization of the molecular pathways of DON biosynthesis in F. graminearum and the environmental factors that influence DON accumulation. In addition, diverse scab resistance traits related to the repression of DON accumulation in plants have been identified, and experimental studies of wheat-pathogen interactions have contributed to understanding detoxification mechanisms in host plants. The present review illustrates and summarizes the molecular networks of DON mycotoxin production in F. graminearum and the methods of DON detoxification in plants based on the current literature, which provides molecular targets for crop improvement programs. This review also comprehensively discusses recent advances and challenges related to genetic engineering-mediated cultivar improvements to strengthen scab resistance. Furthermore, ongoing advancements in genetic engineering will enable the application of these molecular targets to develop more scab-resistant wheat cultivars with DON detoxification traits.