Identification and expression analysis of S-alk(en)yl-L-cysteine sulfoxide lyase isoform genes and determination of allicin contents in Allium species

Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L

Saffron (Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the beneficial economic and medicinal properties of saffron, the regulatory mechanism of the correlation of TFs and genes related to the biosynthesis of the apocarotenoids pathway is less obvious. Realizing these regulatory hierarchies of gene expression networks related to secondary metabolites production events is the main challenge owing to the complex and extensive interactions between the genetic behaviors. Recently, high throughput expression data have been highly feasible for constructing co-regulation networks to reveal the regulated processes and identifying novel candidate hub genes in response to complex processes of the biosynthesis of secondary metabolites. Herein, we performed Weighted Gene Co-expression Network Analysis (WGCNA), a systems biology method, to identify 11 regulated modules and hub TFs related to secondary metabolites. Three specialized modules were found in the apocarotenoids pathway. Several hub TFs were identified in notable modules, including MADS, C2H2, ERF, bZIP, HD-ZIP, and zinc finger protein MYB and HB, which were potentially associated with apocarotenoid biosynthesis. Furthermore, the expression levels of six hub TFs and six co-regulated genes of apocarotenoids were validated with RT-qPCR. The results confirmed that hub TFs specially MADS, C2H2, and ERF had a high correlation (P < 0.05) and a positive effect on genes under their control in apocarotenoid biosynthesis (CCD2, GLT2, and ADH) among different C. sativus ecotypes in which the metabolite contents were assayed. Promoter analysis of the co-expressed genes of the modules involved in apocarotenoids biosynthesis pathway suggested that not only are the genes co-expressed, but also share common regulatory motifs specially related to hub TFs of each module and that they may describe their common regulation. The result can be used to engineer valuable secondary metabolites of C. sativus by manipulating the hub regulatory TFs.

Novel NARC-G1 garlic: comparative allicin quantification with morpho-biochemical & genetic profiling

Abstract Garlic (Allium sativum) is an important cash food crop, and the biotechnology industry has considerable interest in the plant because of its medicinal importance. These medicinal properties are attributed to organosulphur compounds as the accumulation of these compounds varies according to genotype, locality, light quality, and cultivation practices. In this study, we compared a newly developed garlic variety NARC-G1 by National Agricultural Research Centre (NARC), Islamabad, Pakistan with three different garlic cultivars and highlighted the distinctive attributes like phenotypic characteristics, the content of allicin, elemental profile, and gene polymorphism. Phenotypic analysis showed NARC-G1 has significantly higher bulb weight (66.36g ± 18.58), single clove weight (5.87g ± 1.041), and clove width (17.41mm ± 0.95) which directly correlates to the size of the garlic. The analytical analysis showed the highest allicin content (4.82 ± 0.001) in NARC-G1. Genotyping of the alliinase in all four cultivars showed indels in the gene resulting in distinguishable changes in organosulphur compounds’ profile. NARC-G1 is unique from other garlic cultivars and could be the best choice for mass production with proper cultivation and irrigation management. Moreover, for Pakistan NARC-G1 could be a potential contender to earn the industrial benefits with inland cultivation instead of importing garlic alleviating the economic burden.

Plant Secondary Metabolites: The Weapons for Biotic Stress Management

The rise in global temperature also favors the multiplication of pests and pathogens, which calls into question global food security. Plants have developed special coping mechanisms since they are sessile and lack an immune system. These mechanisms use a variety of secondary metabolites as weapons to avoid obstacles, adapt to their changing environment, and survive in less-than-ideal circumstances. Plant secondary metabolites include phenolic compounds, alkaloids, glycosides, and terpenoids, which are stored in specialized structures such as latex, trichomes, resin ducts, etc. Secondary metabolites help the plants to be safe from biotic stressors, either by repelling them or attracting their enemies, or exerting toxic effects on them. Modern omics technologies enable the elucidation of the structural and functional properties of these metabolites along with their biosynthesis. A better understanding of the enzymatic regulations and molecular mechanisms aids in the exploitation of secondary metabolites in modern pest management approaches such as biopesticides and integrated pest management. The current review provides an overview of the major plant secondary metabolites that play significant roles in enhancing biotic stress tolerance. It examines their involvement in both indirect and direct defense mechanisms, as well as their storage within plant tissues. Additionally, this review explores the importance of metabolomics approaches in elucidating the significance of secondary metabolites in biotic stress tolerance. The application of metabolic engineering in breeding for biotic stress resistance is discussed, along with the exploitation of secondary metabolites for sustainable pest management.

Metabolic engineering of the diosgenin biosynthesis pathway in Trigonella foenum-graceum hairy root cultures

Diosgenin as a triterpene with numbers of pharmaceutical applications has been identified in Trigonella foenum-graceum. In this survey, in order to scale up the amount of diosgenin in Fenugreek as a promising alternative of yam, ∆²⁴-reductase as a rate limiting enzyme in diosgenin biosynthesis pathway has been overexpressed by utilizing pBI121 expression plasmid in hairy roots culture platform. The recombinant binary vector pBI121-∆²⁴-reductase was transformed into R. rhizogenes strain ATCC 15834 to induce transgenic hairy roots in "Hamedan" as a low-diosgenin production genotype. In the transgenic hairy roots, the ∆²⁴-reductase expression level was significantly 8.15 times overexpressed comparing to the non-transgenic hairy roots, Nonetheless the Sterol-methyltransferase, as a competitive enzyme, was 6 times downregulated. Furthermore, the expression rate of Squalene synthase, Cycloartenol synthase, C26-Hydroxylase were also increased 1.5, 1.7, 2.9 times higher than those of the non-transgenic hairy roots, respectively. The diosgenin content in the transgenic hairy root was raised 3 times up comparing to the non-transgenic hairy roots, besides it was scaled up 25-fold comparing to the diosgenin amount in "Hamedan" Leaf. As a result, the first metabolic engineering on this pathway was clearly revealed the impact of ∆²⁴ -reductase gene in diosgenin content enhancement.

Current studies and potential future research directions on biological effects and related mechanisms of allicin

Allicin, a thiosulfonate extract from freshly minced garlic, has been reported to have various biological effects on different organs and systems of animals and human. It can reduce oxidative stress, inhibit inflammatory response, resist pathogen infection and regulate intestinal flora. In addition, dozens of studies also demonstrated allicin could reduce blood glucose level, protect cardiovascular system and nervous system, and fight against cancers. Allicin was widely used in disease prevention and health care. However, more investigations on human cohort study are needed to verify the biological or clinical effects of allicin in the future. In this review, we summarized the biological effects of allicin from previous outstanding and valuable studies and provided useful information for future studies on the health effects of allicin.

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium

Allium is one of the well-known genera of the Amaryllidaceae family, which contains over 780 species. Onions, garlic, leeks, and shallots are the most important species of this genus. Allium hirtifolium (shallot) is a rich source of proteins, carbohydrates, lipids, amino acids, and bioactive compounds such as organic sulfur compounds with an expansive range of biological activities and medicinal attributes. To identify the putative compounds and genes involved in the organic sulfur pathway, we applied GC-MS and RNA-seq techniques for the bulb, stem, and flower tissues of A. hirtifolium. The essential oil analysis revealed the maximum amount of sulfur compounds in stem against flower and bulb tissues. Transcriptome profiling showed 6155, 6494, and 4259 DEGs for bulb vs. flower, bulb vs. stem, and flower vs. stem, respectively. Overall, more genes were identified as being up-regulated rather than down-regulated in flower tissue compared to the stem and bulb tissues. Our findings in accordance with other results from different papers, suggest that carbohydrates are vital to bulb formation and development because a high number of identified DEGs (586 genes) were mapped to carbohydrate metabolism. This study has detected the genes in the organic sulfur pathway and indicated that the alliinase gene shows a high variability among different tissues. In general, this study formed a useful genomic resource data to explore tissue-specific sulfur pathway in A. hirtifolium, which is helpful for functional breeding.