Integrative Analysis of Metabolome and Transcriptome Identifies Potential Genes Involved in the Flavonoid Biosynthesis in Entada phaseoloides Stem

Biosynthesis and metabolic engineering of natural sweeteners

Natural sweeteners have attracted widespread attention because they are eco-friendly, healthy, low in calories, and tasty. The demand for natural sweeteners is increasing together with the popularity of green, low-carbon, sustainable development. With the development of synthetic biology, microbial cell factories have emerged as an effective method to produce large amounts of natural sweeteners. This technology has significantly progressed in recent years. This review summarizes the pathways and the enzymes related to the biosynthesis of natural sweeteners, such as mogrosides, steviol glycosides, glycyrrhizin, glycyrrhetinic acid, phlorizin, trilobatin, erythritol, sorbitol, mannitol, thaumatin, monellin, and brazzein. Moreover, it focuses on the research about the microbial production of these natural sweeteners using synthetic biology methods, aiming to provide a reference for future research on the production of natural sweeteners.

Transcriptome and Metabolome Analysis of Low-Pressure Regulation in Saussurea involucrata Leaves

Saussurea involucrata, an endangered medicinal plant, thrives in high mountain regions at altitudes ranging from 3500 to 5000 m. Being a plant that grows at high altitudes means it possesses unique physiological mechanisms and stress-responsive genes that regulate and adapt to the high-altitude environment. While many cold-resistant genes have been cloned and their mechanisms studied, the genes and molecular mechanisms involved in adaptation to hypobaric hypoxia remain largely unexplored. This study conducted transcriptomic and metabolomic analyses on the leaves of S. involucrata under normal atmosphere (101 kPa) and low pressure (60 kPa). A total of 2383 differentially expressed genes (DEGs) and 336 differentially accumulated metabolites (DAMs) were identified utilizing RNA-seq and UPLS-MS techniques. The results indicated that S. involucrata exhibits responses to hypobaric hypoxia environments by engaging in DNA repair, membrane transport, hypoxic response, reproductive processes, and various metabolic activities associated with nutrient uptake and the effective utilization of chemical components. It is worth noting that under low-pressure treatment, flavonoids are predominantly negatively regulated, whereas terpenoids are primarily positively regulated. These findings identify key genes and metabolites in S. involucrata that respond to hypobaric hypoxia treatment, providing a theoretical basis for the development of its medicinal value and for low-altitude cultivation.

Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis

Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content, which has been linked to a variety of pharmacological benefits and crucial health-promoting impacts in humans. The progress in understanding the molecular mechanisms of flavonoid accumulation in this plant has been hindered due to the deficiency of genomic and transcriptomic resources. We utilized a combination of Illumina and Oxford Nanopore Technology (ONT) sequencing to generate a de novo hybrid transcriptome assembly. In total, 126,977 unigenes were characterized, out of which 107,977 were successfully annotated in seven public databases. Within the annotated unigenes, 3,781 were categorized into 58 transcription factor families. Furthermore, we investigated the presence of four valuable flavonoids-quercetin-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, and kaempferol-3-O-β-D-glucoside in 98 samples, using high-performance liquid chromatography. A weighted gene co-expression network analysis identified two co-expression modules, MEpink and MEturquoise, that showed strong positive correlation with flavonoid content. Within these modules, four transcription factor genes (R2R3-MYB, NAC, WD40, and ARF) and four key enzyme-encoding genes (CHI, F3H, PAL, and C4H) emerged as potential hub genes. Among them, the R2R3-MYB (LcsMYB123) as a homologous gene to AtMYB123/TT2, was speculated to play a significant role in flavonol biosynthesis based on phylogenetic analysis. Our findings provided a theoretical foundation for further research into the molecular mechanisms of flavonoid biosynthesis. Additionally, The hybrid transcriptome sequences will serve as a valuable molecular resource for the transcriptional annotation of L. coreana var. sinensis, which will contribute to the improvement of high-flavonoid materials.

Combined analysis of the transcriptome and metabolome provides insights into the fleshy stem expansion mechanism in stem lettuce

As a stem variety of lettuce, the fleshy stem is the main product organ of stem lettuce. The molecular mechanism of fleshy stem expansion in stem lettuce is a complex biological process. In the study, the material accumulation, gene expression, and morphogenesis during fleshy stem expansion process were analyzed by the comparative analysis of metabolome, transcriptome and the anatomical studies. The anatomical studies showed that the occurrence and activity of vascular cambium mainly led to the development of fleshy stems; and the volume of pith cells gradually increased and arranged tightly during the expansion process. A total of 822 differential metabolites and 9,383 differentially expressed genes (DEGs) were identified by the metabolomics and transcriptomics analyses, respectively. These changes significantly enriched in sugar synthesis, glycolysis, and plant hormone anabolism. The expression profiles of genes in the sugar metabolic pathway gradually increased in fleshy stem expansion process. But the sucrose content was the highest in the early stage of fleshy stem expansion, other sugars such as fructose and glucose content increased during fleshy stem expansion process. Plant hormones, including IAA, GA, CTK, and JA, depicted important roles at different stem expansion stages. A total of 1,805 DEGs were identified as transcription factors, such as MYB, bHLH, and bZIP, indicating that these transcription factor families might regulate the fleshy stems expansion in lettuce. In addition, the expression patterns identified by qRT-PCR were consistent with the expression abundance identified by the transcriptome data. The important genes and metabolites identified in the lettuce fleshy stem expansion process will provide important information for the further molecular mechanism study of lettuce fleshy stem growth and development.

Integrative Metabolome and Transcriptome Analysis Reveals the Regulatory Network of Flavonoid Biosynthesis in Response to MeJA in Camelliavietnamensis Huang

Flavonoids are secondary metabolites widely found in plants, which perform various biological activities, such as antiinflammation, antioxidation, antitumor, and so on. Camellia vietnamensis Huang, a species of oil-tea Camellia tree, is an important woody oil crop species widely planted on Hainan Island, which provides health benefits with its high antioxidant activity and abundant flavonoid content. However, very little is known about the overall molecular mechanism of flavonoid biosynthesis in C. vietnamensis Huang. In this study, methyl jasmonate (MeJA) is used as an inducer to change the content of secondary metabolites in C. vietnamensis. Then, the potential mechanisms of flavonoid biosynthesis in C. vietnamensis leaves in response to MeJA were analyzed by metabolomics and transcriptomics (RNA sequencing). The results showed that metabolome analysis detected 104 flavonoids and 74 fatty acyls which showed different expression patterns (increased or decreased expression). It was discovered by KEGG analysis that three differentially accumulated metabolites (cinnamaldehyde, kaempferol and quercitrin) were annotated in the phenylpropanoid biosynthesis (ko00940), flavonoid biosynthesis (ko00941), and flavone and flavonol biosynthesis (ko00944) pathways. In the transcriptome analysis, 35 different genes involved in the synthesis of flavonoids were identified by MapMan analysis. The key genes (PAL, 4CL, CCR, CHI, CHS, C4H, FLS) that might be involved in the formation of flavonoid were highly expressed after 2 h of MeJA treatment. This study provides new insights and data supporting the molecular mechanism underlying the metabolism and synthesis of flavonoids in C. vietnamensis under MeJA treatment.