Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis

Transcriptome wide analysis of MADS box genes in Crocus sativus and interplay of CstMADS19-CstMADS26 in orchestrating apocarotenoid biosynthesis

Flowers of Crocus sativus L. are immensely important not only for arrangement of floral whorls but more because each floral organ is dominated by a different class of specialized compounds. Dried stigmas of C. sativus flowers form commercial saffron, and are known to accumulate unique apocarotenoids like crocin, picrocrocin and safranal. Inspite of being a high value crop, the molecular mechanism regulating flower development in Crocus remains largely unknown. Moreover, it would be very interesting to explore any co-regulatory mechanism which controls floral architecture and secondary metabolic pathways which exist in specific floral organs. Here we report transcriptome wide identification of MADS box genes in Crocus. A total of 39 full length MADS box genes were identified among which three belonged to type I and 36 to type II class. Phylogeny classified them into 11 sub-clusters. Expression pattern revealed some stigma up-regulated genes among which CstMADS19 encoding an AGAMOUS gene showed high expression. Transient over-expression of CstMADS19 in stigmas of Crocus resulted in increased crocin by enhancing expression of pathway genes. Yeast one hybrid assay demonstrated that CstMADS19 binds to promoters of phytoene synthase and carotenoid cleavage dioxygenase 2 genes. Yeast two hybrid and BiFC assays confirmed interaction of CstMADS19 with CstMADS26 which codes for a SEPALATA gene. Co-overexpression of CstMADS19 and CstMADS26 in Crocus stigmas enhanced crocin content more than was observed when genes were expressed individually. Collectively, these findings indicate that CstMADS19 functions as a positive regulator of stigma based apocarotenoid biosynthesis in Crocus.

Potential therapeutic effects of crocin

Crocin, a natural bioactive compound derived from saffron (Crocus sativus) and other Crocus genera, has gained significant attention recently due to its potential therapeutic properties. The multifaceted nature of crocin's biological effects has piqued the interest of researchers and health enthusiasts, prompting further investigations into its mechanisms of action and therapeutic applications. This review article comprehensively explores the emerging evidence supporting crocin's role as a promising ally in protecting against metabolic disorders. The review covers the molecular mechanisms underlying crocin's beneficial effects and highlights its potential applications in preventing and treating diverse pathological conditions. Understanding the mechanisms through which crocin exerts its protective effects could advance scientific knowledge and offer potential avenues for developing novel therapeutic interventions. As we uncover the potential of crocin as a valuable ally in the fight against disorders, it becomes evident that nature's palette holds remarkable solutions for enhancing our health.

A novel mutation in non-constitutive lycopene beta cyclase (CstLcyB2a) from Crocus sativus modulates carotenoid/apocarotenoid content, biomass and stress tolerance in plants

MAIN CONCLUSION

Mutation at A126 in lycopene-β-cyclase of Crocus (CstLcyB2a) sterically hinders its binding of δ-carotene without affecting lycopene binding, thereby diverting metabolic flux towards β-carotene and apocarotenoid biosynthesis. Crocus sativus, commonly known as saffron, has emerged as an important crop for research because of its ability to synthesize unique apocarotenoids such as crocin, picrocrocin and safranal. Metabolic engineering of the carotenoid pathway can prove a beneficial strategy for enhancing the quality of saffron and making it resilient to changing climatic conditions. Here, we demonstrate that introducing a novel mutation at A126 in stigma-specific lycopene-β-cyclase of Crocus (CstLcyB2a) sterically hinders its binding of δ-carotene, but does not affect lycopene binding, thereby diverting metabolic flux towards β-carotene formation. Thus, A126L-CstLcyB2a expression in lycopene-accumulating bacterial strains resulted in enhanced production of β-carotene. Transient expression of A126L-CstLcyB2a in C. sativus stigmas enhanced biosynthesis of crocin. Its stable expression in Nicotiana tabacum enhanced β-branch carotenoids and phyto-hormones such as abscisic acid (ABA) and gibberellic acids (GA's). N. tabacum transgenic lines showed better growth performance and photosynthetic parameters including maximum quantum efficiency (Fv/Fm) and light-saturated capacity of linear electron transport. Exogenous application of hormones and their inhibitors demonstrated that a higher ratio of GA4/ABA has positive effects on biomass of wild-type and transgenic plants. Thus, these findings provide a platform for the development of new-generation crops with improved productivity, quality and stress tolerance.

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.

Comparative analysis of miRNA expression profiles in flowering and non-flowering tissue of Crocus sativus L

Crocus sativus is a valuable plant due to the presence of apocarotenoids in its stigma. Considerable work has been done in the past to understand the apocarotenoid biosynthetic pathway in saffron. However, the reports on understanding the regulation of flowering at the post-transcriptional level are meagre. The study aimed to discover the candidate miRNAs, target genes, transcription factors (TFs), and apocarotenoid biosynthetic pathway genes associated with the regulation and transition of flowering in C. sativus. In the present investigation, miRNA profiling was performed in flowering and non-flowering corms of saffron, along with expression analysis of apocarotenoid genes and transcription factors involved in the synthesis of secondary metabolites. Significant modulation in the expression of miR156, miR159, miR166, miR172, miR395, miR396, miR399, and miR408 gene families was observed. We obtained 36 known miRNAs (26 in flowering and 10 in non-flowering) and 64 novel miRNAs (40 in flowering and 24 in non-flowering) unique to specific tissues in our analysis. TFs, including CsMADS and CsMYb, showed significant modulation in expression in flowering tissue, followed by CsHB. Additionally, the miRNAs were predicted to be involved in carbohydrate metabolism, phytohormone signalling, regulation of flower development, and response to stress, cold, and defence. The comprehensive study has enhanced our understanding of the regulatory machinery comprising factors like phytohormones, abiotic stress, apocarotenoid genes, transcription factors, and miRNAs responsible for the synthesis of apocarotenoids and developmental processes during and after flowering.

"Plant Golden" C. sativus: Qualitative and quantitative analysis of major components in stigmas and petals and their biological activity in vitro

Crocus sativus L. (C. sativus) has its stigma as the main valuable part used. With extremely low production and high prices, stigma is considered a scarce resource. As a result, its petals, considered as by-products, are often discarded, leading to significant waste. We developed a UPLC-Q-Orbitrap HRMS method for qualitative analysis of stigmas and petals and a UHPLC-QQQ-MS/MS method for simultaneous quantification of 9 characteristic active compounds for the first time, and compared their biological activity in vitro. The results indicated that a total of 63 compounds were identified in the petals and stigmas. The content of flavonoids in the petals was significantly superior to that in the stigma, and the content of quercetin in the petals was 50 times higher than that in the stigma. The results of the in vitro evaluation of biological activity indicated that both the petals （•OH: IC50=39.70 mg/mL; DPPH: IC50=28.37 mg/mL; ABTS: IC50=0.9868 mg/mL）and stigma （•OH: IC50=34.41 mg/mL; DPPH: IC50=38.99 mg/mL; ABTS: IC50=3.194 mg/mL）demonstrated comparable antioxidant activities. However, the tyrosinase inhibitory activity in petals （IC50=21.17 mg/mL） was weaker than that in stigma（IC50=1.488 mg/mL）. This study provides a fast, reliable, and efficient analytical method that can be used for the quality assessment of petals as a natural resource and its related products in the food and pharmaceutical industries.

Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites

BACKGROUND

The increasing demand for saffron metabolites in various commercial industries, including medicine, food, cosmetics, and dyeing, is driven by the discovery of their diverse applications. Saffron, derived from Crocus sativus stigmas, is the most expensive spice, and there is a need to explore additional sources to meet global consumption demands. In this study, we focused on yellow-flowering crocuses and examined their tepals to identify saffron-like compounds.

RESULTS

Through metabolomic and transcriptomic approaches, our investigation provides valuable insights into the biosynthesis of compounds in yellow-tepal crocuses that are similar to those found in saffron. The results of our study support the potential use of yellow-tepal crocuses as a source of various crocins (crocetin glycosylated derivatives) and flavonoids.

CONCLUSIONS

Our findings suggest that yellow-tepal crocuses have the potential to serve as a viable excessive source of some saffron metabolites. The identification of crocins and flavonoids in these crocuses highlights their suitability for meeting the demands of various industries that utilize saffron compounds. Further exploration and utilization of yellow-tepal crocuses could contribute to addressing the growing global demand for saffron-related products.

Mining of disease-resistance genes in Crocus sativus based on transcriptome sequencing

Introduction: Crocus sativus L. has an important medicinal and economic value in traditional perennial Chinese medicine. However, due to its unique growth characteristics, during cultivation it is highly susceptible to disease. The absence of effective resistance genes restricts us to breed new resistant varieties of C. sativus. Methods: In present study, comprehensive transcriptome sequencing was introduced to explore the disease resistance of the candidate gene in healthy and corm rot-infected C. sativus. Results and discussion: Totally, 43.72 Gb of clean data was obtained from the assembly to generate 65,337 unigenes. By comparing the gene expression levels, 7,575 differentially expressed genes (DEGs) were primarily screened. A majority of the DEGs were completely in charge of defense and metabolism, and 152 of them were annotated as pathogen recognition genes (PRGs) based on the PGRdb dataset. The expression of some transcription factors including NAC, MYB, and WRKY members, changed significantly based on the dataset of transcriptome sequencing. Therefore, this study provides us some valuable information for exploring candidate genes involved in the disease resistance in C. sativus.

Transcriptome wide identification, characterization and expression analysis of PHD gene family in Crocus sativus

Crocus sativus L., of the Iridaceae family, yields world's most prized spice, saffron. Saffron is well known for its distinctive aroma, odour and colour, which are imputed to the presence of some specific glycosylated apocarotenoids. Even though the main biosynthetic pathway and most of the enzymes leading to apocarotenoid production have been identified, the regulatory mechanisms that govern the developmental stage and tissue specific production of apocarotenoids in Crocus remain comparatively unravelled. Towards this, we report identification, and characterization of plant homeodomain (PHD) finger transcription factor family in Crocus sativus. We also report cloning and characterisation of CstPHD27 from C. sativus. CstPHD27 recorded highest expression in stigma throughout flower development. CstPHD27 exhibited expression pattern which corresponded to the apocarotenoid accumulation in Crocus stigmas. CstPHD27 is nuclear localized and transcriptionally active in yeast Y187 strain. Over-expression of CstPHD27 in Crocus stigmas enhanced apocarotenoid content by upregulating the biosynthetic pathway genes. This report on PHD finger transcription factor family from C. sativus may offer a basis for elucidating role of this gene family in this traditionally and industrially prized crop.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01410-3.

CstMYB1R1, a REVEILLE-8-like transcription factor, regulates diurnal clock-specific anthocyanin biosynthesis and response to abiotic stress in Crocus sativus L

KEY MESSAGE

CstMYB1R1 acts as a positive regulator of Crocus anthocyanin biosynthesis and abiotic stress tolerance which was experimentally demonstrated through molecular analysis and over-expression studies in Crocus and Nicotiana. Regulatory mechanics of flavonoid/anthocyanin biosynthesis in Crocus floral tissues along the diurnal clock has not been studied to date. MYB proteins represent the most dominant, functionally diverse and versatile type of plant transcription factors which regulate key metabolic and physiological processes in planta. Transcriptome analysis revealed that MYB family is the most dominant transcription factor family in C. sativus. Considering this, a MYB-related REVEILLE-8 type transcription factor, CstMYB1R1, was explored for its possible role in regulating Crocus flavonoid and anthocyanin biosynthetic pathway. CstMYB1R1 was highly expressed in Crocus floral tissues, particularly tepals and its expression was shown to peak at dawn and dusk time points. Anthocyanin accumulation also peaked at dawn and dusk and was minimum at night. Moreover, the diurnal expression pattern of CstMYB1R1 was shown to highly correlate with Crocus ANS/LDOX gene expression among the late anthocyanin pathway genes. CstMYB1R1 was shown to be nuclear localized and transcriptionally active. CstMYB1R1 over-expression in Crocus tepals enhanced anthocyanin levels and upregulated transcripts of Crocus flavonoid and anthocyanin biosynthetic pathway genes. Yeast one hybrid (Y1H) and GUS reporter assay confirmed that CstMYB1R1 interacts with the promoter of Crocus LDOX gene to directly regulate its transcription. In addition, the expression of CstMYB1R1 in Nicotiana plants significantly enhanced flavonoid and anthocyanin levels and improved their abiotic stress tolerance. The present study, thus, confirmed positive role of CstMYB1R1 in regulating Crocus anthocyanin biosynthetic pathway in a diurnal clock-specific fashion together with its involvement in the regulation of abiotic stress response.

CstPIF4 Integrates Temperature and Circadian Signals and Interacts with CstMYB16 to Repress Anthocyanins in Crocus

Crocus sativus has emerged as an important crop because it is the only commercial source of saffron that contains unique apocarotenoids. Saffron is composed of dried stigmas of Crocus flower and constitutes the most priced spice of the world. Crocus floral organs are dominated by different classes of metabolites. While stigmas are characterized by the presence of apocarotenoids, tepals are rich in flavonoids and anthocyanins. Therefore, an intricate regulatory network might play a role in allowing different compounds to dominate in different organs. Work so far done on Crocus is focussed on apocarotenoid metabolism and its regulation. There are no reports describing the regulation of flavonoids and anthocyanins in Crocus tepals. In this context, we identified an R2R3 transcription factor, CstMYB16, which resembles subgroup 4 (SG4) repressors of Arabidopsis. CstMYB16 is nuclear localized and acts as a repressor. Overexpression of CstMYB16 in Crocus downregulated anthocyanin biosynthesis. The C2/EAR motif was responsible for the repressor activity of CstMYB16. CstMYB16 binds to the promoter of the anthocyanin biosynthetic pathway gene (LDOX) and reduces its expression. CstMYB16 also physically interacts with CstPIF4, which in turn is regulated by temperature and circadian clock. Thus, CstPIF4 integrates these signals and forms a repressor complex with CstMYB16, which is involved in the negative regulation of anthocyanin biosynthesis in Crocus. Independent of CstPIF4, CstMYB16 also represses CstPAP1 expression, which is a component of the MYB-bHLH-WD40 (MBW) complex and positively controls anthocyanin biosynthesis. This is the first report on identifying and describing regulators of anthocyanin biosynthesis in Crocus.

Transcriptome Insights into Candidate Genes of the SWEET Family and Carotenoid Biosynthesis during Fruit Growth and Development in Prunus salicina 'Huangguan'

The Chinese plum (Prunus salicina L.) is a fruit tree belonging to the Rosaceae family, native to south-eastern China and widely cultivated throughout the world. Fruit sugar metabolism and color change is an important physiological behavior that directly determines flavor and aroma. Our study analyzed six stages of fruit growth and development using RNA-seq, yielding a total of 14,973 DEGs, and further evaluation of key DEGs revealed a focus on sugar metabolism, flavonoid biosynthesis, carotenoid biosynthesis, and photosynthesis. Using GO and KEGG to enrich differential genes in the pathway, we selected 107 differential genes and obtained 49 significant differential genes related to glucose metabolism. The results of the correlation analyses indicated that two genes of the SWEET family, evm.TU.Chr1.3663 (PsSWEET9) and evm.TU.Chr4.676 (PsSWEET2), could be closely related to the composition of soluble sugars, which was also confirmed in the ethylene treatment experiments. In addition, analysis of the TOP 20 pathways between different growth stages and the green stage, as well as transient overexpression in chili, suggested that capsanthin/capsorubin synthase (PsCCS) of the carotenoid biosynthetic pathway contributed to the color change of plum fruit. These findings provide an insight into the molecular mechanisms involved in the ripening and color change of plum fruit.

The apocarotenoid production in microbial biofactories: An overview

Carotenoids are a vast group of natural pigments that come in a variety of colors ranging from red to orange. Apocarotenoids are derived from these carotenoids, which are hormones, pigments, retinoids, and volatiles employed in the textiles, cosmetics, pharmaceutical, and food industries. Due to the high commercial value and poor natural host abundance, they are significantly undersupplied. Microbes like Saccharomyces cerevisiae and Escherichia coli act as heterologous hosts for apocarotenoid production. This article briefly reviews categories of apocarotenoids, their biosynthetic pathway commencing from the MVA and MEP, its significance, the tool enzymes for apocarotenoid biosynthesis like CCDs, their biotechnological production in microbial factories, and future perspectives.

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.

Understanding saffron biology using omics- and bioinformatics tools: stepping towards a better Crocus phenome

Saffron is a unique plant in many aspects, and its cellular processes are regulated at multiple levels. The genetic makeup in the form of eight chromosome triplets (2n = 3x = 24) with a haploid genetic content (genome size) of 3.45 Gbp is decoded into different types of RNA by transcription. The RNA then translates into peptides and functional proteins, sometimes involving post-translational modifications too. The interactions of the genome, transcriptome, proteome and other regulatory molecules ultimately result in the complex set of primary and secondary metabolites of saffron metabolome. These complex interactions manifest in the form of a set of traits 'phenome' peculiar to saffron. The phenome responds to the environmental changes occurring in and around saffron and modify its response in respect of growth, development, disease response, stigma quality, apocarotenoid biosynthesis, and other processes. Understanding these complex relations between different yet interconnected biological activities is quite challenging in saffron where classical genetics has a very limited role owing to its sterility, and the absence of a whole-genome sequence. Omics-based technologies are immensely helpful in overcoming these limitations and developing a better understanding of saffron biology. In addition to creating a comprehensive picture of the molecular mechanisms involved in apocarotenoid synthesis, stigma biogenesis, corm activity, and flower development, omics-technologies will ultimately lead to the engineering of saffron plants with improved phenome.

SlWRKY35 positively regulates carotenoid biosynthesis by activating the MEP pathway in tomato fruit

Carotenoids are vital phytonutrients widely recognised for their health benefits. Therefore, it is vital to thoroughly investigate the metabolic regulatory network underlying carotenoid biosynthesis and accumulation to open new leads towards improving their contents in vegetables and crops. The outcome of our study defines SlWRKY35 as a positive regulator of carotenoid biosynthesis in tomato. SlWRKY35 can directly activate the expression of the 1-deoxy-d-xylulose 5-phosphate synthase (SlDXS1) gene to reprogramme metabolism towards the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway, leading to enhanced carotenoid accumulation. We also show that the master regulator SlRIN directly regulates the expression of SlWRKY35 during tomato fruit ripening. Compared with the SlLCYE overexpression lines, coexpression of SlWRKY35 and SlLCYE can further enhance lutein production in transgenic tomato fruit, indicating that SlWRKY35 represents a potential target towards designing innovative metabolic engineering strategies for carotenoid derivatives. In addition to providing new insights into the metabolic regulatory network associated with tomato fruit ripening, our data define a new tool for improving fruit content in specific carotenoid compounds.

Insights from the analysis of draft genome sequence of Crocus sativus L

Saffron (Crocus sativus L.) is the low yielding plant of medicinal and economic importance. Therefore, it is of interest to report the draft genome sequence of C. sativus. The draft genome of C. sativus has been assembled using Illumina sequencing and is 3.01 Gb long covering 84.24% of genome. C. sativus genome annotation identified 53,546 functional genes (including 5726 transcription factors), 862,275 repeats and 964,231 SSR markers. The genes involved in the apocarotenoids biosynthesis pathway (crocin, crocetin, picrocrocin, and safranal) were found in the draft genome analysis.

Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining

A robust workflow for the identification of miRNAs and their targets in saffron was developed. MicroRNA-mediated gene regulation in saffron is potentially involved in several biological processes, including the biosynthesis of highly valuable apocarotenoids. Saffron (Crocus sativus L.) is the most expensive spice in the world and a major source of apocarotenoids. Even though miRNAs (20-24 nt non-coding small RNAs) are important regulators of gene expression at transcriptional and post-transcriptional levels, their role in saffron has not been thoroughly investigated. As a result, a workflow for computational identification of miRNAs and their targets can be useful to uncover the regulatory networks underlying biological processes in this valuable plant. The efficiency of several assembly tools such as Trans-ABySS, Trinity, Bridger, rnaSPAdes, and EvidentialGene was evaluated based on both reference-based and reference-free metrics using transcriptome data. A reliable workflow for computational identification of miRNAs and their targets in saffron was described. The EvidentialGene was found to be the most efficient de novo transcriptome assembler for saffron as a complex triploid model, followed by the Trinity. In total, 66 miRNAs from 19 different families that target 2880 genes, including several transcription factors involved in the flowering transition, were identified. Three of the identified targets were involved in the terpenoids backbone biosynthesis. CsCCD and CsUGT genes involved in the apocarotenoids biosynthetic pathway were targeted by csa-miR156g and csa-miR156b-3p, revealing a unique post-transcriptional regulation dynamic in saffron. The identified miRNAs and their targets add to our understanding of the many biological roles of miRNAs in saffron and shed new light on the control of the apocarotenoid biosynthetic pathway in this valuable plant.

Crocus transcription factors CstMYB1 and CstMYB1R2 modulate apocarotenoid metabolism by regulating carotenogenic genes

Two MYB genes have been identified which regulate apocarotenoid metabolism in Crocus sativus. Apocarotenoids like crocin, picrocrocin and safranal are restricted to genus Crocus and are synthesized by oxidative cleavage of zeaxanthin followed by glycosylation reactions. In Crocus sativus, these apocarotenoids are synthesized in stigma part of the flower in developmentally regulated manner. Most of the genes of apocarotenoid pathway are known, however, the mechanism that regulates its tissue and stage specific biosynthesis remains elusive. MYB family was identified as the largest transcription factor family from Crocus transciptome which indicated its possible role in apocarotenoid regulation besides regulating other metabolic pathways. Towards this, we started with identification of 150 MYB genes from Crocus transcriptome databases. The phylogenetic analysis of Crocus MYB genes divided them into 27 clusters. Domain analysis resulted in identification of four groups of MYBs depending upon the number of R repeats present. Expression profiling indicated that 12 MYBs are upregulated in stigma out of which expression of four genes CstMYB1, CstMYB14, CstMYB16 and CstMYB1R2 correlated with crocin accumulation. Transient overexpression of two nuclear localized MYB genes (CstMYB1 and CstMYB1R2) in Crocus confirmed their role in regulating carotenoid metabolism. Yeast-one-hybrid confirmed that CstMYB1 binds to carotenoid cleavage dioxygenase 2 (CCD2) promoter while CstMYB1R2 binds to phytoene synthase (PSY) and CCD2 promoters. Overall, our study established that CstMYB1 and CstMYB1R2 regulate apocarotenoid biosynthesis by directly binding to promoters of pathway genes.

A New Glycosyltransferase Enzyme from Family 91, UGT91P3, Is Responsible for the Final Glucosylation Step of Crocins in Saffron (Crocus sativus L.)

Crocetin is an apocarotenoid formed from the oxidative cleavage of zeaxanthin, by the carotenoid cleavage enzymes CCD2 (in Crocus species) and specific CCD4 enzymes in Buddleja davidii and Gardenia jasminoides. Crocetin accumulates in the stigma of saffron in the form of glucosides and crocins, which contain one to five glucose molecules. Crocetin glycosylation was hypothesized to involve at least two enzymes from superfamily 1 UDP-sugar dependent glycosyltransferases. One of them, UGT74AD1, produces crocins with one and two glucose molecules, which are substrates for a second UGT, which could belong to the UGT79, 91, or 94 families. An in silico search of Crocus transcriptomes revealed six candidate UGT genes from family 91. The transcript profiles of one of them, UGT91P3, matched the metabolite profile of crocin accumulation, and were co-expressed with UGT74AD1. In addition, both UGTs interact in a two-hybrid assay. Recombinant UGT91P3 produced mostly crocins with four and five glucose molecules in vitro, and in a combined transient expression assay with CCD2 and UGT74AD1 enzymes in Nicotiana benthamiana. These results suggest a role of UGT91P3 in the biosynthesis of highly glucosylated crocins in saffron, and that it represents the last missing gene in crocins biosynthesis.

Transcriptomic analysis of saffron at different flowering stages using RNA sequencing uncovers cytochrome P450 genes involved in crocin biosynthesis

Saffron is a well-known Chinese traditional herb, and crocin biosynthesis is related to the yield and quality of saffron. This study aimed to screen differentially expressed genes (DEGs) in saffron at different flowering stages and identify cytochrome P450 (CYP) genes involved in crocin biosynthesis. Saffron samples at different flowering stages were used for RNA sequencing, and DEGs between the samples at three days before the flowering stage (- 3da) and two days after the flowering stage (+ 2da) were screened. Thereafter, significantly differentially expressed CYP genes were identified, and CYP gene expression at different flowering stages and in various tissues of saffron was determined using real-time quantitative polymerase chain reaction (RT-qPCR). After sequencing and analysis, 1508 DEGs between the samples at - 3da and + 2da were identified, including 487 upregulated and 1021 downregulated genes, which were enriched in 16 biological processes, 5 cellular components, 3 molecular functions, and 11 KEGG pathways, including protein processing in endoplasmic reticulum, pentose and glucuronate interconversions, starch and sucrose metabolism, estrogen signaling pathway, and mitogen-activated protein kinase signaling pathway. In addition, 12 significantly differentially expressed CYP genes were identified. The RT-qPCR results showed that CYP76C4, CYP72A15, CYP72A219, CYP97B2, CYP714C2, CYP71A1, CYP94C1, and CYP86A8 were all expressed in the pistils, and CYP72A219, CYP72A15, CYP97B2, CYP71A1, and CYP86A8 were highly expressed in the pistils. Our study established a transcriptome library of saffron and found that CYP72A219, CYP72A15, CYP97B2, CYP71A1, and CYP86A8 may be candidates involved crocin biosynthesis in saffron.

The effect of salt stress on the production of apocarotenoids and the expression of genes related to their biosynthesis in saffron

Saffron stigmas are widely used as food additives and as traditional medicine in Iran and many other countries. The unique taste, flavor and pharmaceutical properties of saffron stigmas are due to the presence of three apocarotenoids secondary metabolites crocin, picrocrocin and safranal. There is limited knowledge about the effect of environmental stresses on the metabolism of apocarotenoids in saffron. We analyzed the content of crocin and picrocrocin and the expression of key genes of apocarotenoid biosynthesis pathways (CsCCD2, CsCCD4, CsUGT2, CsCHY-β and CsLCYB) in saffron plants exposed to moderate (90 mM) and high (150 mM) salt (NaCl) concentrations. Measuring ion concentrations in leaves showed an increased accumulation of Na⁺ and decreased uptake of K⁺ in salt treated compared to control plants indicating an effective salt stress. HPLC analysis of apocarotenoids revealed that crocin production was significantly halted (P < 0.05) with increasing salt concentration while picrocrocin level did not change with moderate salt but significantly dropped by high salt concentration. Real-time PCR analysis revealed a progressive decrease in transcript levels of CsUGT2 and CsLCYB genes with increasing salt concentration (P < 0.05). The expression of CsCCD2 and CsCHY-β tolerated moderate salt concentration but significantly downregulated with high salt concentration. CsCCD4 however responded differently to salt concentration being decreased with moderate salt but increased at higher salt concentration. Our result suggested that salt stress had an adverse effect on the production of saffron apocarotenoids and it is likely influencing the quality of saffron stigma produced.

Nutritional and health beneficial properties of saffron (Crocus sativus L): a comprehensive review

Saffron (Crocus sativus L., family Iridaceae) is used traditionally for medicinal purpose in Chinese, Ayurvedic, Persian and Unani medicines. The bioactive constituents such as apocarotenoids, monoterpenoids, flavonoids, phenolic acids and phytosterols are widely investigated in experimental and clinical studies for a wide range of therapeutic effects, especially on the nervous system. Some of the active constituents of saffron have high bioavailability and bioaccessibility and ability to pass the blood-brain barrier. Multiple preclinical and clinical studies have supported neuroprotective, anxiolytic, antidepressant, learning and memory-enhancing effect of saffron and its bioactive constituents (safranal, crocin, and picrocrocin). Thus, this plant and its active compounds could be a beneficial medicinal food ingredient in the formation of drugs targeting nervous system disorders. This review focuses on phytochemistry, bioaccessibility, bioavailability, and bioactivity of phytochemicals in saffron. Furthermore, the therapeutic effect of saffron against different nervous system disorders has also been discussed in detail.

Prospects and progress on crocin biosynthetic pathway and metabolic engineering

Crocins are a group of highly valuable apocarotenoid-derived pigments mainly produced in Crocus sativus stigmas and Gardenia jasminoides fruits, which display great pharmacological activities for human health, such as anticancer, reducing the risk of atherosclerosis, and preventing Alzheimer's disease. However, traditional sources of crocins are no longer sufficient to meet current demands. The recent clarification of the crocin biosynthetic pathway opens up the possibility of large-scale production of crocins by synthetic metabolic engineering methods. In this review, we mainly introduce the crocin biosynthetic pathway, subcellular route, related key enzymes, and its synthetic metabolic engineering, as well as its challenges and prospects, with a view to providing useful references for further studies on the synthetic metabolic engineering of crocins.

The Sensory Significance of Apocarotenoids in Wine: Importance of Carotenoid Cleavage Dioxygenase 1 (CCD1) in the Production of β-Ionone

Olfactory cues are key drivers of our multisensory experiences of food and drink. For example, our perception and enjoyment of the flavour and taste of a wine is primarily steered by its aroma. Making sense of the underlying smells that drive consumer preferences is integral to product innovation as a vital source of competitive advantage in the marketplace, which explains the intense interest in the olfactory component of flavour and the sensory significance of individual compounds, such as one of the most important apocarotenoids for the bouquet of wine, β-ionone (violet and woody notes). β-Ionone is formed directly from β-carotene as a by-product of the actions of carotenoid cleavage dioxygenases (CCDs). The biological production of CCDs in microbial cell factories is one way that important aroma compounds can be generated on a large scale and with reduced costs, while retaining the 'natural' moniker. The CCD family includes the CCD1, CCD2, CCD4, CCD7 and CCD8; however, the functions, co-dependency and interactions of these CCDs remain to be fully elucidated. Here, we review the classification, actions and biotechnology of CCDs, particularly CCD1 and its action on β-carotene to produce the aromatic apocarotenoid β-ionone.

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)

Saffron, derived from the stigma of Crocus sativus, is not only a valuable traditional Chinese medicine but also the expensive spice and dye. Its yield and quality are seriously influenced by its flowering transition. However, the molecular regulatory mechanism of the flowering transition in C. sativus is still unknown. In this study, we performed morphological, physiological and transcriptomic analyses using apical bud samples from C. sativus during the floral transition process. Morphological results indicated that the flowering transition process could be divided into three stages: an undifferentiated period, the early flower bud differentiation period, and the late flower bud differentiation period. Sugar, gibberellin (GA₃), auxin (IAA) and zeatin (ZT) levels were steadily upregulated, while starch and abscisic acid (ABA) levels were gradually downregulated. Transcriptomic analysis showed that a total of 60 203 unigenes were identified, among which 19 490 were significantly differentially expressed. Of these, 165 unigenes were involved in flowering and were significantly enriched in the sugar metabolism, hormone signal transduction, cell cycle regulatory, photoperiod and autonomous pathways. Based on the above analysis, a hypothetical model for the regulatory networks of the saffron flowering transition was proposed. This study lays a theoretical basis for the genetic regulation of flowering in C. sativus.

A high-throughput platform for interpretation of metabolite profile data from pepper (Capsicum) fruits of 13 phenotypes associated with different fruit maturity states

Nowadays, novel tools have been developed for efficient analysis and visualization of large-scale metabolite profile data associated with metabolic pathways. A high-throughput platform using PathVisio 3 combined with multivariate analysis is proposed for the first time. Additionally, this is the first analysis of the relationships among terpenoids monoterpene, sesquiterpene, triterpene, and tetraterpene during pepper fruit ripening, and their changes. This platform was successfully applied to interpret large-scale data related to 131 metabolites from mature and immature fruits of 13 pepper phenotypes. The carotenoid-derived volatiles, such as dihydroactinidiolide and β-ionone were closely correlated with carotenoids, indicating that the synthesis and degradation of carotenoids occurred in pepper fruit mature stage. Using PathVisio 3, the metabolic changes in pathway could be presented quickly, revealing the accumulation of stress-related metabolites, such as proline, capsaicin, and phenylalanine, in the mature stage. This approach could provide useful information about comprehensive biochemical regulation of fruit ripening.

De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

Senna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.

Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus

Crocus sativus, containing remarkably amounts of crocin, picrocrocin and safranal, is the source of saffron with tremendous medicinal, economic and cultural importance. Here, we present a high-quality full-length transcriptome of the sterile triploid C. sativus, using the PacBio SMRT sequencing technology. This yields 31,755 high-confidence predictions of protein-coding genes, with 50.1% forming paralogous gene pairs. Analysis on distribution of Ks values suggests that the current genome of C. sativus is probably a product resulting from at least two rounds of whole-genome duplication (WGD) events occurred at ~28 and ~114 million years ago (Mya), respectively. We provide evidence demonstrating that the recent β WGD event confers a major impact on family expansion of secondary metabolite genes, possibly leading to an enhanced accumulation of three distinct compounds: crocin, picrocrocin and safranal. Phylogenetic analysis unravels that the founding member (CCD2) of CCD enzymes necessary for the biosynthesis of apocarotenoids in C. sativus might be evolved from the CCD1 family via the β WGD event. Based on the gene expression profiling, CCD2 is found to be expressed at an extremely high level in the stigma. These findings may shed lights on further genomic refinement of the characteristic biosynthesis pathways and promote germplasm utilization for the improvement of saffron quality.

Differential interaction of Or proteins with the PSY enzymes in saffron

Colored apocarotenoids accumulate at high concentrations in few plant species, where display a role in attraction of pollinators and seed dispersers. Among these apocarotenoids, crocins accumulate at high concentrations in the stigma of saffron and are responsible for the organoleptic and medicinal properties of this spice. Phytoene synthase and Orange protein are key for carotenoid biosynthesis and accumulation. We previously isolated four phytoene synthase genes from saffron with differential roles in carotenoid and apocarotenoid biosynthesis. However, the implications of Orange genes in the regulation of apocarotenoid accumulation are unknown. Here, we have identified two Orange genes from saffron, with different expression patterns. CsOr-a was mainly expressed in vegetative tissues and was induced by light and repressed by heat stress. Both CsOr-a and CsOr-b were expressed in stigmas but showed a different profile during the development of this tissue. The interactions of CsOr-a and CsOr-b were tested with all the four phytoene synthase proteins from saffron and with CsCCD2. None interactions were detected with CCD2 neither with the phytoene synthase 2, involved in apocarotenoid biosynthesis in saffron. The obtained results provide evidence of different mechanisms regulating the phytoene synthase enzymes in saffron by Orange for carotenoid and apocarotenoid accumulation in saffron.

Single-molecule real-time transcript sequencing identified flowering regulatory genes in Crocus sativus

Background

Saffron crocus (Crocus sativus) is a valuable spice with medicinal uses in gynaecopathia and nervous system diseases. Identify flowering regulatory genes plays a vital role in increasing flower numbers, thereby resulting in high saffron yield.

Results

Two full length transcriptome gene sets of flowering and non-flowering saffron crocus were established separately using the single-molecule real-time (SMRT) sequencing method. A total of sixteen SMRT cells generated 22.85 GB data and 75,351 full-length saffron crocus unigenes on the PacBio RS II panel and further obtained 79,028 SSRs, 72,603 lncRNAs and 25,400 alternative splicing (AS) events. Using an Illumina RNA-seq platform, an additional fifteen corms with different flower numbers were sequenced. Many differential expression unigenes (DEGs) were screened separately between flowering and matched non-flowering top buds with cold treatment (1677), flowering top buds of 20 g corms and non-flowering top buds of 6 g corms (1086), and flowering and matched non-flowering lateral buds (267). A total of 62 putative flower-related genes that played important roles in vernalization (VRNs), gibberellins (G3OX, G2OX), photoperiod (PHYB, TEM1, PIF4), autonomous (FCA) and age (SPLs) pathways were identified and a schematic representation of the flowering gene regulatory network in saffron crocus was reported for the first time. After validation by real-time qPCR in 30 samples, two novel genes, PB.20221.2 (p = 0.004, r = 0.52) and PB.38952.1 (p = 0.023, r = 0.41), showed significantly higher expression levels in flowering plants. Tissue distribution showed specifically high expression in flower organs and time course expression analysis suggested that the transcripts increasingly accumulated during the flower development period.

Conclusions

Full-length transcriptomes of flowering and non-flowering saffron crocus were obtained using a combined NGS short-read and SMRT long-read sequencing approach. This report is the first to describe the flowering gene regulatory network of saffron crocus and establishes a reference full-length transcriptome for future studies on saffron crocus and other Iridaceae plants.

UGT709G1: a novel uridine diphosphate glycosyltransferase involved in the biosynthesis of picrocrocin, the precursor of safranal in saffron (Crocus sativus)

Saffron, a spice derived from the dried red stigmas of Crocus sativus, is one of the oldest natural food additives. The flowers have long red stigmas, which store significant quantities of the glycosylated apocarotenoids crocins and picrocrocin. The apocarotenoid biosynthetic pathway in saffron starts with the oxidative cleavage of zeaxanthin, from which crocins and picrocrocin are derived. In the processed stigmas, picrocrocin is converted to safranal, giving saffron its typical aroma. By a targeted search for differentially expressed uridine diphosphate glycosyltransferases (UGTs) in Crocus transcriptomes, a novel apocarotenoid glucosyltransferase (UGT709G1) from saffron was identified. Biochemical analyses revealed that UGT709G1 showed a high catalytic efficiency toward 2,6,6-trimethyl-4-hydroxy-1-carboxaldehyde-1-cyclohexene (HTCC), making it suited for the biosynthesis of picrocrocin, the precursor of safranal. The role of UGT709G1 in picrocrocin/safranal biosynthesis was supported by the absence or presence of gene expression in a screening for HTCC and picrocrocin production in different Crocus species and by a combined transient expression assay with CsCCD2L in Nicotiana benthamiana leaves. The identification of UGT709G1 completes one of the most highly valued specialized metabolic biosynthetic pathways in plants and provides novel perspectives on the industrial production of picrocrocin to be used as a flavor additive or as a pharmacological constituent.

Transcriptome analysis reveals novel enzymes for apo-carotenoid biosynthesis in saffron and allows construction of a pathway for crocetin synthesis in yeast

Crocus sativus is generally considered the source of saffron spice which is rich in apo-carotenoid compounds such as crocins, crocetin, picrocrocin, and safranal, which possess effective pharmacological activities. However, little is known about the exact genes involved in apo-carotenoid biosynthesis in saffron and the potential mechanism of specific accumulation in the stigma. In this study, we integrated stigmas at different developmental stages to perform in-depth transcriptome and dynamic metabolomic analyses to discover the potential key catalytic steps involved in apo-carotenoid biosynthesis in saffron. A total of 61 202 unigenes were obtained, and 28 regulators and 32 putative carotenogenic genes were captured after the co-expression network analysis. Moreover, 15 candidate genes were predicted to be closely related to safranal and crocin production, in which one aldehyde dehydrogenase (CsALDH3) was validated to oxidize crocetin dialdehyde into crocetin and a crocetin-producing yeast strain was created. In addition, a new branch pathway that catalyses the conversion of geranyl-geranyl pyrophosphate to copalol and ent-kaurene by the class II diterpene synthase CsCPS1 and three class I diterpene synthases CsEKL1/2/3 were investigated for the first time. Such gene to apo-carotenoid landscapes illuminate the synthetic charactersistics and regulators of apo-carotenoid biosynthesis, laying the foundation for a deep understanding of the biosynthesis mechanism and metabolic engineering of apo-carotenoids in plants or microbes.

Diverse biological effects of glycosyltransferase genes from Tartary buckwheat

BACKGROUND

Tartary buckwheat (Fagopyrum tataricum) is an edible cereal crop whose sprouts have been marketed and commercialized for their higher levels of anti-oxidants, including rutin and anthocyanin. UDP-glucose flavonoid glycosyltransferases (UFGTs) play an important role in the biosynthesis of flavonoids in plants. So far, few studies are available on UFGT genes that may play a role in tartary buckwheat flavonoids biosynthesis. Here, we report on the identification and functional characterization of seven UFGTs from tartary buckwheat that are potentially involved in flavonoid biosynthesis (and have varying effects on plant growth and development when overexpressed in Arabidopsis thaliana.) RESULTS: Phylogenetic analysis indicated that the potential function of the seven FtUFGT proteins, FtUFGT6, FtUFGT7, FtUFGT8, FtUFGT9, FtUFGT15, FtUFGT40, and FtUFGT41, could be divided into three Arabidopsis thaliana functional subgroups that are involved in flavonoid biosynthesis of and anthocyanin accumulation. A significant positive correlation between FtUFGT8 and FtUFGT15 expression and anthocyanin accumulation capacity was observed in the tartary buckwheat seedlings after cold stress. Overexpression in Arabidopsis thaliana showed that FtUFGT8, FtUFGT15, and FtUFGT41 significantly increased the anthocyanin content in transgenic plants. Unexpectedly, overexpression of FtUFGT6, while not leading to enhanced anthocyanin accumulation, significantly enhanced the growth yield of transgenic plants. When wild-type plants have only cotyledons, most of the transgenic plants of FtUFGT6 had grown true leaves. Moreover, the growth speed of the oxFtUFGT6 transgenic plant root was also significantly faster than that of the wild type. At later growth, FtUFGT6 transgenic plants showed larger leaves, earlier twitching times and more tillers than wild type, whereas FtUFGT15 showed opposite results.

CONCLUSIONS

Seven FtUFGTs were isolated from tartary buckwheat. FtUFGT8, FtUFGT15, and FtUFGT41 can significantly increase the accumulation of total anthocyanins in transgenic plants. Furthermore, overexpression of FtUFGT6 increased the overall yield of Arabidopsis transgenic plants at all growth stages. However, FtUFGT15 shows the opposite trend at later growth stage and delays the growth speed of plants. These results suggested that the biological function of FtUFGT genes in tartary buckwheat is diverse.

Biologically active compounds and pharmacological activities of species of the genus Crocus: A review

The present article is the first comprehensive review on the chemical composition and pharmacological activities of the raw materials of Crocus species. In the present review, data on chemical constituents and pharmacological profile of Crocus sativus stigmas, as well as of other plant parts (perianth, stamens, leaves, corms) of different Crocus spp. are given. This review discusses all the classes of compounds (carotenoids, flavonoids, anthocyanins, terpenoids, phenol carboxylic acids, etc.) detected in raw materials of Crocus plants providing information on the current state of knowledge on phytochemicals of Crocus species. Almost all structural formulas of the compounds identified and isolated from Crocus species are given; all compounds are presented in accordance with the types of the studied raw materials. The latest hypotheses relating to the biosynthesis pathways of the main biologically active compounds of saffron (crocin, picrocrocin, safranal), as well as chemotaxonomy of Crocus genus are briefly summarized. The present review discusses the most thoroughly studied pharmacological activities (namely, antioxidant, antiparasitic, hypolipidemic, antihypertensive, immunomodulatory, antimicrobial, antitumor, cytotoxic, antidepressant) of saffron stigmas extracts, of its individual phytochemicals (safranal, crocin, crocetin), as well as pharmacological activities of raw materials of other Crocus species. This comprehensive review will be informative for scientists searching for new properties of saffron stigmas, as well as for saffron producers, since the present review highlights the prospects for the use of waste products in the production of the expensive spice. In addition, the present review provides information on pharmacological properties and composition of other Crocus species as promising medicinal and food plants. In the present review the emphasis will be put on the chemical constituents of Crocus species and the intraspecies variation in phytochemicals and pharmacological activities.

Arbuscular Mycorrhizal Fungi Modulate the Crop Performance and Metabolic Profile of Saffron in Soilless Cultivation

Saffron (Crocus sativus L.) is cultivated worldwide. Its stigmas represent the highest-priced spice and contain bioactive compounds beneficial for human health. Saffron cultivation commonly occurs in open field, and spice yield can vary greatly, from 0.15 to 1.5 g m−2, based on several agronomic and climatic factors. In this study, we evaluated saffron cultivation in soilless systems, where plants can benefit from a wealth of nutrients without competition with pathogens or stresses related to nutrient-soil interaction. In addition, as plant nutrient and water uptake can be enhanced by the symbiosis with arbuscular mycorrhizal fungi (AMF), we also tested two inocula: a single species (Rhizophagus intraradices) or a mixture of R. intraradices and Funneliformis mosseae. After one cultivation cycle, we evaluated the spice yield, quality (ISO category), antioxidant activity, and bioactive compound contents of saffron produced in soilless systems and the effect of the applied AMF inocula. Spice yield in soilless systems (0.55 g m−2) was on average with that produced in open field, while presented a superior content of several health-promoting compounds, such as polyphenols, anthocyanins, vitamin C, and elevated antioxidant activity. The AMF symbiosis with saffron roots was verified by light and transmission electron microscopy. Inoculated corms showed larger replacement corms (+50% ca.). Corms inoculated with R. intraradices performed better than those inoculated with the mix in terms of spice quality (+90% ca.) and antioxidant activity (+88% ca.). Conversely, the mixture of R. intraradices and F. mosseae increased the polyphenol content (+343% ca.). Thus, soilless systems appeared as an effective alternative cultivation strategy for the production of high quality saffron. Further benefits can be obtained by the application of targeted AMF-based biostimulants.

Multi-species transcriptome analyses for the regulation of crocins biosynthesis in Crocus

BACKGROUND

Crocins are soluble apocarotenoids that mainly accumulate in the stigma tissue of Crocus sativus and provide the characteristic red color to saffron spice, in addition to being responsible for many of the medicinal properties of saffron. Crocin biosynthesis and accumulation in saffron is developmentally controlled, and the concentration of crocins increases as the stigma develops. Until now, little has been known about the molecular mechanisms governing crocin biosynthesis and accumulation. This study aimed to identify the first set of gene regulatory processes implicated in apocarotenoid biosynthesis and accumulation.

RESULTS

A large-scale crocin-mediated RNA-seq analysis was performed on saffron and two other Crocus species at two early developmental stages coincident with the initiation of crocin biosynthesis and accumulation. Pairwise comparison of unigene abundance among the samples identified potential regulatory transcription factors (TFs) involved in crocin biosynthesis and accumulation. We found a total of 131 (up- and downregulated) TFs representing a broad range of TF families in the analyzed transcriptomes; by comparison with the transcriptomes from the same developmental stages from other Crocus species, a total of 11 TF were selected as candidate regulators controlling crocin biosynthesis and accumulation.

CONCLUSIONS

Our study generated gene expression profiles of stigmas at two key developmental stages for apocarotenoid accumulation in three different Crocus species. Differential gene expression analyses allowed the identification of transcription factors that provide evidence of environmental and developmental control of the apocarotenoid biosynthetic pathway at the molecular level.

Transcript profiling of carotenoid/apocarotenoid biosynthesis genes during corm development of saffron (Crocus sativus L.)

The dried stigmas of saffron constitute the world's costliest spice. Saffron has many therapeutic applications due to the presence of apocarotenoids. The latter are synthesized at different stages of development, and the biosynthetic pathway involves several genes encoding different enzymes. In order to understand the differential expression of various genes of the pathway, eight distinct developmental stages (S1-early to S8-late) were identified. The corms were assorted into three groups (I, II, and III) based on corm weight. Expression profiles of 12 carotenoid/apocarotenoid genes were studied. The expression of all genes was minimum/least in groups I and II corms during bud development. Lowest expression of carotenogenic genes (CsPSY, CsPDS, CsZDS, CsCRTISO, CsLYC-β1, CsLYC-ε, CsBCH2, and CsNCED) was observed during early stages (S1-S3) of corm growth (dormant period). In group III corms, increased expression of apocarotenoid genes (CsZCO, CsCCD2, CsUGT, and CsALDH) was observed during S4 to S8 stages (reproductive period, floral differentiation). Besides, expression profiles of genes in apical and axillary buds were also examined. Of all the genes studied, apocarotenoid biosynthesis genes (CsBCH2, CsZCO, CsCCD2, CsALDH, and CsUGT) were found to be upregulated in apical bud than in the axillary bud. The results indicated that interaction of phytohormones and sugars, mother corm reserves and the influence of internal and external factors may be contributing to the growth of saffron corm/bud. The study has laid a foundation for further research on the molecular mechanisms underlying bud dormancy/growth in saffron.

Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis

Crocins, the red soluble apocarotenoids of saffron, accumulate in the flowers of Crocus species in a developmental and tissue-specific manner. In Crocus sieberi, crocins accumulate in stigmas but also in a distinct yellow tepal sector, which we demonstrate contains chromoplast converted from amyloplasts. Secondary metabolites were analysed by LC-DAD-HRMS, revealing the progressive accumulation of crocetin and crocins in the yellow sector, which were also localized in situ by Raman microspectroscopy. To understand the underlying mechanisms of crocin biosynthesis, we sequenced the C. sieberi tepal transcriptome of two differentially pigmented sectors (yellow and white) at two developmental stages (6 and 8) by Illumina sequencing. A total of 154 million high-quality reads were generated and assembled into 248,099 transcripts. Differentially expressed gene analysis resulted in the identification of several potential candidate genes involved in crocin metabolism and regulation. The results provide a first profile of the molecular events related to the dynamics of crocetin and crocin accumulation during tepal development, and present new information concerning apocarotenoid biosynthesis regulators and their accumulation in Crocus. Further, reveals genes that were previously unknown to affect crocin formation, which could be used to improve crocin accumulation in Crocus plants and the commercial quality of saffron spice.

Microarray analysis of differentially expressed genes in L929 mouse fibroblast cells exposed to leptin and hypoxia

Leptin and hypoxia are pro-fibrotic factors involved in fibrogenesis, however, the gene expression profiles remain to be fully elucidated. The aim of the present study was to investigate the regulatory roles of leptin and hypoxia on the L929 mouse fibroblast cell line. The cells were assigned to a normoxia, normoxia with leptin, hypoxia, and hypoxia with leptin group. The cDNA expression was detected using an Agilent mRNA array platform. The differentially expressed genes (DEGs) in response to leptin and hypoxia were identified using reverse transcription-quantitative polymerase chain reaction analysis, followed by clustering analysis, Gene Ontology analysis and pathway analysis. As a result, 54, 1,507 and 1,502 DEGs were found in response to leptin, hypoxia and the two combined, respectively, among which 52 (96.30%), 467 (30.99%) and 495 (32.96%) of the DEGs were downregulated. The most significant functional terms in response to leptin were meiosis I for biological process (P=0.0041) and synaptonemal complex for cell component (P=0.0013). Only one significant pathway responded to leptin, which was axon guidance (P=0.029). Flow cytometry confirmed that leptin promoted L929 cell proliferation. The most significant functional terms in response to hypoxia were ion binding for molecular function (P=7.8621E-05), glucose metabolic process for biological process (P=0.0008) and cell projection part for cell component (P=0.003). There were 12 pathways, which significantly responded to hypoxia (P<0.05) and the pathway with the highest significance was the chemokine signaling pathway (P=0.0001), which comprised 28 genes, including C-C motif ligand (CCL)1, C-X-C motif ligand (CXCL)9, CXCL10, son of sevenless homolog 1, AKT serine/threonine kinase 2, Rho-associated protein kinase 1, vav guanine nucleotide exchange factor 1, CCL17, arrestin β1 and C-C motif chemokine receptor 2. In conclusion, the present study showed that leptin and hypoxia altered the profiles of gene expression in L929 cells. These findings not only extend the cell spectrum of leptin on cell proliferation, but also improve current understanding of hypoxia in fibroblast cells.

Daylily protein constituents of the pollen and stigma a proteomics approach

This study was aimed at the identification and quantification of the protein components of the pollen grains in parallel with the distal stigmatic tissue of tetraploid cultivars. Proteomes were analyzed using iTRAQ 4plex labeling, peptides separation by online RP-nano-LC and analysis by ESI-MS/MS. Protein identification and quantification were made using the Asparagales database as a reference. A total of 524,037 MS/MS spectra were produced from pollen and stigma samples. From these, a total of 8368 peptides wereidentified corresponding to 994 unique peptides and 432 protein groups. Among them, 128 differentially expressed proteins were retained for further analysis. In absence of the daylily genome availability, we exploited numerous databases and bioinformatics resources to exploring the putative biological functions of these proteins. The profile of differentially expressed proteins suggests an important representation of functions associated to the signalling and response against endogenous and environmental stresses, including several enzymes implicated in the biosynthesis of antibiotics. The abundance in stigma of several structural proteins of the ribosomal sub-units as well as of the core histones suggest that the translation processes and the regulation of gene expression in stigma is a more active mechanism than in pollen. In addition, pollen prioritizes the synthesis of fructose and glucose as opposed to sucrose in stigma as a source of energy. Finally, the modulated proteins in Hemerocallis point to several pathways that give potential clues concerning the molecular mechanisms underlying the functions of the pollen and the stigmatic fluid in daylily reproduction.

Transcriptome wide identification, phylogenetic analysis, and expression profiling of zinc-finger transcription factors from Crocus sativus L

Crocus sativus belongs to Iridaceae family and is the only plant species which produces apocarotenoids like crocin, picrocrocin, and safranal in significant quantities. Besides their organoleptic properties, Crocus apocarotenoids have been found to possess remarkable pharmacological potential. Although apocarotenoid biosynthetic pathway has been worked out to a great degree, but the mechanism that regulates the tissue and developmental stage-specific production of Crocus apocarotenoids is not known. To identify the genes regulating apocarotenoid biosynthesis in Crocus, transcriptome wide identification of zinc-finger transcription factors was undertaken. 81 zinc-finger transcription factors were identified which grouped into eight subfamilies. C2H2, C3H, and AN20/AN1 were the major subfamilies with 29, 20, and 14 members, respectively. Expression profiling revealed CsSAP09 as a potential candidate for regulation of apocarotenoid biosynthesis. CsSAP09 was found to be highly expressed in stigma at anthesis stage corroborating with the accumulation pattern of apocarotenoids. CsSAP09 was nuclear localized and activated reporter gene transcription in yeast. It was highly induced in response to oxidative, salt and dehydration stresses, ABA and methyl jasmonate. Furthermore, upstream region of CsSAP09 was found to contain stress and light responsive elements. To our knowledge, this is the first report on the study of a gene family in C. sativus and may provide basic insights into the putative role of zinc finger genes. It may also serve as a valuable resource for functional characterization of these genes aimed towards unraveling their role in regulation of apocarotenoid biosynthesis.

Functional Characterization of CsBGlu12, a β-Glucosidase from Crocus sativus, Provides Insights into Its Role in Abiotic Stress through Accumulation of Antioxidant Flavonols

Glycosylation and deglycosylation are impressive mechanisms that allow plants to regulate the biological activity of an array of secondary metabolites. Although glycosylation improves solubility and renders the metabolites suitable for transport and sequestration, deglycosylation activates them to carry out biological functions. Herein, we report the functional characterization of CsBGlu12, a β-glucosidase from Crocus sativus. CsBGlu12 has a characteristic glucoside hydrolase 1 family (α/β)₈ triose-phosphate isomerase (TIM) barrel structure with a highly conserved active site. In vitro enzyme activity revealed that CsBGlu12 catalyzes the hydrolysis of flavonol β-glucosides and cello-oligosaccharides. Site-directed mutagenesis of any of the two conserved catalytic glutamic acid residues (Glu²⁰⁰ and Glu⁴¹⁴) of the active site completely abolishes the β-glucosidase activity. Transcript analysis revealed that Csbglu12 is highly induced in response to UV-B, dehydration, NaCl, methyl jasmonate, and abscisic acid treatments indicating its possible role in plant stress response. Transient overexpression of CsBGlu12 leads to the accumulation of antioxidant flavonols in Nicotiana benthamiana and confers tolerance to abiotic stresses. Antioxidant assays indicated that accumulation of flavonols alleviated the accretion of reactive oxygen species during abiotic stress conditions. β-Glucosidases are known to play a role in abiotic stresses, particularly dehydration through abscisic acid; however, their role through accumulation of reactive oxygen species (ROS) scavenging flavonols has not been established. Furthermore, only one β-glucosidase 12 homolog has been characterized so far. Therefore, this work presents an important report on characterization of CsBGlu12 and its role in abiotic stress through ROS scavenging.

In silico identification of miRNAs and their target genes and analysis of gene co-expression network in saffron (Crocus sativus L.) stigma

As an aromatic and colorful plant of substantive taste, saffron (Crocus sativus L.) owes such properties of matter to growing class of the secondary metabolites derived from the carotenoids, apocarotenoids. Regarding the critical role of microRNAs in secondary metabolic synthesis and the limited number of identified miRNAs in C. sativus, on the other hand, one may see the point how the characterization of miRNAs along with the corresponding target genes in C. sativus might expand our perspectives on the roles of miRNAs in carotenoid/apocarotenoid biosynthetic pathway. A computational analysis was used to identify miRNAs and their targets using EST (Expressed Sequence Tag) library from mature saffron stigmas. Then, a gene co- expression network was constructed to identify genes which are potentially involved in carotenoid/apocarotenoid biosynthetic pathways. EST analysis led to the identification of two putative miRNAs (miR414 and miR837-5p) along with the corresponding stem- looped precursors. To our knowledge, this is the first report on miR414 and miR837-5p in C. sativus. Co-expression network analysis indicated that miR414 and miR837-5p may play roles in C. sativus metabolic pathways and led to identification of candidate genes including six transcription factors and one protein kinase probably involved in carotenoid/apocarotenoid biosynthetic pathway. Presence of transcription factors, miRNAs and protein kinase in the network indicated multiple layers of regulation in saffron stigma. The candidate genes from this study may help unraveling regulatory networks underlying the carotenoid/apocarotenoid biosynthesis in saffron and designing metabolic engineering for enhanced secondary metabolites.

De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis

Saffron (Crocus sativus L.) is commonly known as world’s most expensive spice with rich source of apocarotenoids and possesses magnificent medicinal properties. To understand the molecular basis of apocarotenoid biosynthesis/accumulation, we performed transcriptome sequencing from five different tissues/organs of C. sativus using Illumina platform. After comprehensive optimization of de novo transcriptome assembly, a total of 105, 269 unique transcripts (average length of 1047 bp and N50 length of 1404 bp) were obtained from 206 million high-quality paired-end reads. Functional annotation led to the identification of many genes involved in various biological processes and molecular functions. In total, 54% of C. sativus transcripts could be functionally annotated using public databases. Transcriptome analysis of C. sativus revealed the presence of 16721 SSRs and 3819 transcription factor encoding transcripts. Differential expression analysis revealed preferential/specific expression of many transcripts involved in apocarotenoid biosynthesis in stigma. We have revealed the differential expression of transcripts encoding for transcription factors (MYB, MYB related, WRKY, C2C2-YABBY and bHLH) involved in secondary metabolism. Overall, these results will pave the way for understanding the molecular basis of apocarotenoid biosynthesis and other aspects of stigma development in C. sativus.

Overexpression of Crocus carotenoid cleavage dioxygenase, CsCCD4b, in Arabidopsis imparts tolerance to dehydration, salt and oxidative stresses by modulating ROS machinery

Apocarotenoids modulate vital physiological and developmental processes in plants. These molecules are formed by the cleavage of carotenoids, a reaction catalyzed by a family of enzymes called carotenoid cleavage dioxygenases (CCDs). Apocarotenoids like β-ionone and β-cyclocitral have been reported to act as stress signal molecules during high light stress in many plant species. In Crocus sativus, these two apocarotenoids are formed by enzymatic cleavage of β-carotene at 9, 10 and 7, 8 bonds by CsCCD4 enzymes. In the present study three isoforms of CsCCD4 were subjected to molecular modeling and docking analysis to determine their substrate specificity and all the three isoforms displayed high substrate specificity for β-carotene. Further, expression of these three CsCCD4 isoforms investigated in response to various stresses revealed that CsCCD4a and CsCCD4b exhibit enhanced expression in response to dehydration, salt and methylviologen, providing a clue towards their role in mediating plant defense response. This was confirmed by overexpressing CsCCD4b in Arabidopsis. The transgenic plants developed longer roots and possessed higher number of lateral roots. Further, overexpression of CsCCD4b imparted enhanced tolerance to salt, dehydration and oxidative stresses as was evidenced by higher survival rate, increased relative root length and biomass in transgenic plants as compared to wild type. Transgenic plants also displayed higher activity and expression of reactive oxygen species (ROS) metabolizing enzymes. This indicates that β-ionone and β-cyclocitral which are enzymatic products of CsCCD4b may act as stress signals and mediate reprogramming of stress responsive genes which ultimately leads to plant defense.