Bioinformatics study of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) genes in Solanaceae

Differential roles of Cassia tora 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase in trade-off between plant growth and drought tolerance

Due to global climate change, drought is emerging as a major threat to plant growth and agricultural productivity. Abscisic acid (ABA) has been implicated in plant drought tolerance, however, its retarding effects on plant growth cannot be ignored. The reactions catalyzed by 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) proteins are critical steps within the isoprenoid biosynthesis in plants. Here, five DXS (CtDXS1-5) and two DXR (CtDXR1-2) genes were identified from Cassia tora genome. Based on multiple assays including the phylogeny, cis-acting element, expression pattern, and subcellular localization, CtDXS1 and CtDXR1 genes might be potential candidates controlling the isoprenoid biosynthesis. Intriguingly, CtDXS1 transgenic plants resulted in drought tolerance but retardant growth, while CtDXR1 transgenic plants exhibited both enhanced drought tolerance and increased growth. By comparison of β-carotene, chlorophyll, abscisic acid (ABA) and gibberellin 3 (GA3) contents in wild-type and transgenic plants, the absolute contents and (or) altered GA3/ABA levels were suggested to be responsible for the balance between drought tolerance and plant growth. The transcriptome of CtDXR1 transgenic plants suggested that the transcript levels of key genes, such as DXS, 9-cis-epoxycarotenoid dioxygenases (NCED), ent-kaurene synthase (KS) and etc, involved with chlorophyll, β-carotene, ABA and GA3 biosynthesis were induced and their contents increased accordingly. Collectively, the trade-off effect induced by CtDXR1 was associated with redesigning architecture in phytohormone homeostasis and thus was highlighted for future breeding purposes.

Transcriptome Analyses Reveal the Aroma Terpeniods Biosynthesis Pathways of Primula forbesii Franch. and the Functional Characterization of the PfDXS2 Gene

Primula forbesii Franch. is a unique biennial herb with a strong floral fragrance, making it an excellent material for studying the aroma characteristics of the genus Primula. The floral scent is an important ornamental trait that facilitates fertilization. However, the molecular mechanism regulating the floral scent in Primula is unknown. In order to better understand the biological mechanisms of floral scents in this species, this study used RNA sequencing analysis to discuss the first transcriptome sequence of four flowering stages of P. forbesii, which generated 12 P. forbesii cDNA libraries with 79.64 Gb of clean data that formed 51,849 unigenes. Moreover, 53.26% of the unigenes were annotated using public databases. P. forbesii contained 44 candidate genes covering all known enzymatic steps for the biosynthesis of volatile terpenes, the major contributor to the flower's scent. Finally, 1-deoxy-d-xylulose 5-phosphate synthase gene of P. forbesii (PfDXS2, MK370094), the first key enzyme gene in the 2-c-methyl-d-erythritol 4-phosphate (MEP) pathway of terpenoids, was cloned and functionally verified using virus-induced gene silencing (VIGs). The results showed that PfDXS2-silencing significantly reduced the relative concentrations of main volatile terpenes. This report is the first to present molecular data related to aroma metabolites biosynthesis pathways and the functional characterization of any P. forbesii gene. The data on RNA sequencing provide comprehensive information for further analysis of other plants of the genus Primula.

Metabolic and transcriptomic analyses elucidate a novel insight into the network for biosynthesis of carbohydrate and secondary metabolites in the stems of a medicinal orchid Dendrobium nobile

Dendrobium nobile is an important medicinal and nutraceutical herb. Although the ingredients of D. nobile have been identified as polysaccharides, alkaloids, amino acids, flavonoids and bibenzyls, our understanding of the metabolic pathways that regulate the synthesis of these compounds is limited. Here, we used transcriptomic and metabolic analyses to elucidate the genes and metabolites involved in the biosynthesis of carbohydrate and several secondary metabolites in the stems of D. nobile. A total of 1005 metabolites and 31,745 genes were detected in the stems of D. nobile. The majority of these metabolites and genes were involved in the metabolism of carbohydrates (fructose, mannose, glucose, xylulose and starch), while some were involved in the metabolism of secondary metabolites (alkaloids, β-tyrosine, ferulic acid, 4-hydroxybenzoate and chrysin). Our predicted regulatory network indicated that five genes (AROG, PYK, DXS, ACEE and HMGCR) might play vital roles in the transition from carbohydrate to alkaloid synthesis. Correlation analysis identified that six genes (ALDO, PMM, BGLX, EGLC, XYLB and GLGA) were involved in carbohydrate metabolism, and two genes (ADT and CYP73A) were involved in secondary metabolite biosynthesis. Our analyses also indicated that phosphoenol-pyruvate (PEP) was a crucial bridge that connected carbohydrate to alkaloid biosynthesis. The regulatory network between carbohydrate and secondary metabolite biosynthesis established will provide important insights into the regulation of metabolites and biological systems in Dendrobium species.

Characterization of the 1-Deoxy-D-xylulose 5-Phosphate synthase Genes in Toona ciliata Suggests Their Role in Insect Defense

The first enzyme, 1-Deoxy-D-xylulose-5-phosphate synthase (DXS), in the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway for isoprenoid precursor biosynthesis has been reported to function differently according to species. However, the current state of knowledge about this gene family in Toona ciliata is limited. The TcDXS gene family was identified from the whole genome of T. ciliata by firstly using bioinformatics analysis. Then, the phylogenetic tree was built and the promoter cis-elements were predicted. Six DXS genes were identified and divided into three groups, which had similar domains and gene structure. They are located on five different chromosomes and encode products that do not vary much in size. An analysis of the cis-acting elements revealed that TcDXS genes possessed light, abiotic stress, and hormone responsive elements. Ultimately, TcDXS1/2/5 was cloned for an in-depth analysis of their subcellular localization and expression patterns. The subcellular localization results of TcDXS1/2/5 showed that they were located in the chloroplast envelope membranes. Based on tissue-specific analyses, TcDXS1/2/5 had the highest expression in mature leaves. Under Hypsipyla robusta stress, their different expressions indicated that these genes may have insect-resistance functions. This research provides a theoretical basis for further functional verification of TcDXSs in the future, and a new concept for breeding pest-resistant T. ciliata.

Cloning and functional analysis of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) in Santalum album L

The commercial value of Santalum album L. lies in its aromatic heartwood and essential oil. Sesquiterpenes are the main components of sandal essential oil, and these are synthesized through the plant's mevalonate (MVA) and methylerythritol phosphate (MEP) pathways. In this study, the first key rate-limiting enzyme, 1-deoxy-D-xylulose-5-phosphate synthase (SaDXS), was investigated to provide a theoretical molecular basis for the sandalwood MEP sesquiterpene biosynthetic pathway. The biofunctions of SaDXS were also analyzed. SaDXS promoters were successfully cloned from a seven-year-old S. album tree. SaDXS1A/1B promoter activity was verified by a β-glucuronidase (GUS) assay and by analyzing cis-acting elements of the promoters, which carried light- and methyl jasmonate (MeJA)-responsive signals. In an experiment involving yellow S. album seedlings, exposure to light upregulated SaDXS1A/1B expression and increased chlorophyll and carotenoid contents when overexpressed in Arabidopsis thaliana. Analysis of the expression of SaDXS1A/1B and SaSSy, key genes of santalol biosynthesis, revealed SaDXS1A expression in all tissues whereas SaDXS1B was expressed in tissues that contained photosynthetic pigments, such as stems, leaves and flowers. Sandal seedlings exogenously treated with two hormones, MeJA and ethylene, revealed similar expression patterns for SaDXS1A/1B and SaSSy. Sandal seedlings were treated with an inhibitor of DXS, clomazone, but showed no significant changes in the contents of α-santalene, β-santalene and α-santalol between treatment and control groups. These results suggest that SaDXS1A/1B play a role in the synthesis of sandalwood sesquiterpenes, providing carbon for downstream secondary metabolites. SaDXS1A/1B also play a role in the biosynthesis of chlorophyll, carotenoids, and primary metabolites.

Control of resource allocation between primary and specialized metabolism in glandular trichomes

Plant specialized metabolites are often synthesized and stored in dedicated morphological structures such as glandular trichomes, resin ducts, or laticifers where they accumulate in large concentrations. How this high productivity is achieved is still elusive, in particular, with respect to the interface between primary and specialized metabolism. Here, we focus on glandular trichomes to survey recent progress in understanding how plant metabolic cell factories manage to balance homeostasis of essential central metabolites while producing large quantities of compounds that constitute a metabolic sink. In particular, we review the role of gene duplications, transcription factors and photosynthesis.

Molecular Cloning and Differential Gene Expression Analysis of 1-Deoxy-D-xylulose 5-Phosphate Synthase (DXS) in Andrographis paniculata (Burm. f) Nees

Andrographis paniculata 1-deoxy-D-xylulose-5-phosphate synthase (ApDXS) gene (GenBank Accession No MG271749.1) was isolated and cloned from leaves for the first time. Expression of ApDXS gene was carried out in Escherichia coli Rosetta cells. Tissue-specific ApDXS gene expression by quantitative RT-PCR (qRT-PCR) revealed maximum fold expression in the leaves followed by stem and roots. Further, the differential gene expression profile of Jasmonic acid (JA)-elicited in vitro adventitious root cultures showed enhanced ApDXS expression compared to untreated control cultures. A. paniculata 3-hydroxy-3-methylglutaryl-coenzyme A reductase (ApHMGR) gene expression was also studied where it was up-regulated by JA elicitation but showed lower expression compared to ApDXS. The highest expression of both genes was found at 25 µm JA elicitation followed by 50 µm. HPLC data indicated that the transcription levels were correlated with increased andrographolide accumulation. The peak level of andrographolide accumulation was recorded at 25 μM JA (9.38-fold) followed by 50 µM JA (7.58-fold) in elicitation treatments. The in silico generated ApDXS 3D model revealed 98% expected amino acid residues in the favored and 2% in the allowed regions of the Ramachandran plot with 92% structural reliability. Further, prediction of conserved domains and essential amino acids [Arg (249, 252, 255), Asn (307) and Ser (247)] involved in ligand/inhibitor binding was carried out by in silico docking studies. Our present findings will generate genomic information and provide a blueprint for future studies of ApDXS and its role in diterpenoid biosynthesis in A. paniculata.