Integrating transcriptomic and metabolomic analysis of hormone pathways in Acer rubrum during developmental leaf senescence

Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Mechanism of Red Maple (Acer rubrum L.) Leaf Coloring

This study employed a combination of ultraviolet spectrophotometry, LC-ESI-MS/MS system, and RNA-sequencing technology; the extracts and isolation of total RNA from the red and yellow leaf strains of red maple (Acer rubrum L.) at different developmental stages were subjected to an intercomparison of the dynamic content of chlorophyll and total anthocyanin, flavonoid metabolite fingerprinting, and gene expression. The metabonomic results indicated that one hundred and ninety-two flavonoids were identified, which could be classified into eight categories in the red maple leaves. Among them, 39% and 19% were flavones and flavonols, respectively. The metabolomic analysis identified 23, 32, 24, 24, 38, and 41 DAMs in the AR1018r vs. AR1031r comparison, the AR1018r vs. AR1119r comparison, the AR1031r vs. AR1119r comparison, the AR1018y vs. AR1031y comparison, the AR1018y vs. AR1119y comparison, and the AR1031y vs. AR1119y comparison, respectively. In total, 6003 and 8888 DEGs were identified in AR1018r vs. AR1031r comparison and in the AR1018y vs. AR1031y comparison, respectively. The GO and KEGG analyses showed that the DEGs were mainly involved in plant hormone signal transduction, flavonoid biosynthesis, and other metabolite metabolic processes. The comprehensive analysis revealed that caffeoyl-CoA 3-O-methyltransferase (Cluster-28704.45358 and Cluster-28704.50421) was up-regulated in the red strain but down-regulated in the yellow strain, while Peonidin 3-O-glucoside chloride and Pelargonidin 3-O-beta-D-glucoside were up-regulated in both the red and yellow strains. By successfully integrating the analyses on the behavior of pigment accumulation, dynamics of flavonoids, and differentially expressed genes with omics tools, the regulation mechanisms underlying leaf coloring in red maple at the transcriptomic and metabolomic levels were demonstrated, and the results provide valuable information for further research on gene function in red maple.

Polyamines effectively mitigate senescence in persistent leaves of Berginia ciliata - a novel model system

Plant leaves provide a unique insight into the changes that occur in organs, tissues and cells as they approach senescence. As part of the parental outlay, plants instigate leaf senescence to reallocate resources from older tissues to new organs towards the termination of the growing season. The aim of crop breeding initiatives is to optimize senescence for specific species. Considering hormonal regulation and their crosstalk during leaf senescence through integration of developmental signals, this work examines the efficacy of polyamines (PAs) in modulating several biochemical and physiological aspects with an ultimate aim to delay leaf senescence in leaf discs of Berginia ciliata (Haw.) sternb. Leaf discs were treated with putrescine (Put), spermidine (Spd) and spermine (Spm) at 20μM, 20μM and 15μM concentration, respectively. A set of leaf discs kept in distilled water served as the control. Leaf discs treated with PAs were green and fresh by about 4 days compared to the control, thus exhibited delayed senescence. This delayed leaf senescence corroborated with the maintenance of high activity of reactive oxygen species (ROS) scavenging antioxidant enzymes viz , superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and higher content of chlorophylls. A marked increase was also observed in membrane stability and soluble proteins in leaf discs treated with PAs. Exogenous PAs reduced oxidative stress in the leaf discs, as revealed by lower malondialdehyde (MDA) level, which is manifested as reduced lipid peroxidation (LPO). Improved membrane stability was proportional to lower LPO, as measured by the membrane stability index (MSI).

Effects of plant age on antioxidant activity and endogenous hormones in Alpine Elymus sibiricus of the Tibetan Plateau

Elymus sibiricus L. is a perennial forage species that has potential to serve as a forage source in livestock grazing systems. However, E. sibiricus has been shown to have a rapid and substantial reduction of aboveground biomass and seed yield after 3 or 4 years and an accelerated aging process. To determine possible aging mechanisms, we planted E. sibiricus seeds in triplicate blocks in 2012, 2015, and 2016, respectively, and harvested samples of leaves and roots at the jointing and heading stages in 2018 and 2019 to determine oxidative indices and endogenous hormones. The fresh aboveground biomass of 4- and 5-year old plants declined by 34.2% and 52.4% respectively compared with 3-year old plants, and the seed yield declined by 12.7% and 34.1%, respectively. The water content in leaves was 51.7%, 43.3%, and 35.6%, and net photosynthesis was 7.73, 6.35, and 2.08 µmol/m²·s in 3-, 4-, and 5-year old plants, respectively. The superoxide anion radical generation rate in leaves and roots did not show any aging pattern. There was a non-significant increase in malondialdehyde concentration with plant age, particularly in leaves and roots at the heading stage in 2019. The superoxide dismutase activity showed a declining trend with age of plant roots at the jointing stage in both 2018 and 2019. The peroxidase activity declined with plant age in both leaves and roots, for example, and the catalase activity in roots 4- and 7-year old plants declined by 13.8% and 0.85%, respectively, compared to 3-year old plants at the heading stage in 2018. Therefore, the reduced capacity of the antioxidant system may lead to oxidative stress during plant aging process. Overall, the concentrations of plant hormones, auxin (IAA), gibberellin (GA), zeatin (ZT), and abscisic acid (ABA) were significantly lower in roots than in leaves. The IAA concentration in leaves and roots exhibited different patterns with plant age. The ZT concentrations in leaves of 3-year old plants was 2.39- and 2.62-fold of those in 4- and 7-year old plants, respectively at the jointing stage, and in roots, the concentration declined with plant age. The changes in the GA concentration with plant age varied between the physiological stages and between years. The ABA concentrations appeared to increase with plant age, particularly in leaves. In conclusion, the aging process of E. sibiricus was apparently associated with an increase in oxidative stress, a decrease of ZT and an increase of ABA, particularly in roots. These findings highlight the effects of plant age on the antioxidant and endogenous hormone activity of E. sibiricus. However, these plant age-related trends showed variations between plant physiological stages and between harvest years that needs to be researched in the future to develop strategies to manage this forage species.

Comparison of Antioxidant Properties and Metabolite Profiling of Acer pseudoplatanus Leaves of Different Colors

Acer pseudoplatanus (maple) is a widely grown ornamental plant. In addition to its ornamental and ecological value, it also has potentially high economic value. It is a rich source of polyphenols and exhibits antioxidant activity. However, the relationship between polyphenol content and antioxidant activity in maple leaves of different colors (green, yellow, and red) has not yet been investigated. In this study, the total polyphenol (TP), total flavonoid (TFlav), tannin (TET), chlorophyll a and b (Chl a and b), total anthocyanin (TAN), and total carotene (TAC) contents in maple leaves of different colors were evaluated. Their antioxidant activities were determined based on the inhibition of lipid oxidation, DPPH scavenging, ferric ion-reducing antioxidant power, and iron-chelating abilities. The concentrations of TP, TET, TFlav, TAN, and TAC in red maple leaves were higher than those in green and yellow maple leaves. In addition, red maple leaves showed a higher antioxidant effect than the leaves of the other two colors. We observed that antioxidant activity was positively correlated with TP, TFlav, and TAN and negatively correlated with Chl a and b. Finally, we analyzed the metabolites of the different colored (i.e., green, yellow, and red) maple leaves using gas chromatography/mass spectrometry (GC/MS) and found that the metabolite profile significantly varied between the different colors. These results suggest that red leaves are a good source of polyphenols and antioxidants and have potential use in the development of functional foods and medicinal applications.

The chromosome-scale genome provides insights into pigmentation in Acer rubrum

Acer rubrum L. is one of the most prevalent ornamental species of the genus Acer, due to its straight and tall stems and beautiful leaf colors. For this study, the Oxford Nanopore platform and Hi-C technology were employed to obtain a chromosome-scale genome for A. rubrum. The genome size of A. rubrum was 1.69 Gb with an N50 of 549.44 Kb, and a total of 39 pseudochromosomes were generated with a 99.61% genome. The A. rubrum genome was predicted to have 64644 genes, of which 97.34% were functionally annotated. Genome annotation identified 67.14% as the transposable element (TE) repeat sequence, with long terminal repeats (LTR) being the richest (55.68%). Genome evolution analysis indicated that A. rubrum diverged from A. yangbiense ∼6.34 million years ago. We identified 13 genes related to pigment synthesis in A. rubrum leaves, where the expressions of four ArF3'H genes were consistent with the synthesis of cyanidin (a key pigment) in red leaves. Correlation analysis verified that the pigmentation of A. rubrum leaves was under the coordinated regulation of non-structural carbohydrates and hormones. The genomic sequence of A. rubrum will facilitate genomic breeding research for this species, while providing the valuable utilization of Aceraceae resources.

Comparative transcriptomic and metabolic profiling provides insight into the mechanism by which the autophagy inhibitor 3-MA enhances salt stress sensitivity in wheat seedlings

BACKGROUND

Salt stress hinders plant growth and production around the world. Autophagy induced by salt stress helps plants improve their adaptability to salt stress. However, the underlying mechanism behind this adaptability remains unclear. To obtain deeper insight into this phenomenon, combined metabolomics and transcriptomics analyses were used to explore the coexpression of differentially expressed-metabolite (DEM) and gene (DEG) between control and salt-stressed wheat roots and leaves in the presence or absence of the added autophagy inhibitor 3-methyladenine (3-MA).

RESULTS

The results indicated that 3-MA addition inhibited autophagy, increased ROS accumulation, damaged photosynthesis apparatus and impaired the tolerance of wheat seedlings to NaCl stress. A total of 14,759 DEGs and 554 DEMs in roots and leaves of wheat seedlings were induced by salt stress. DEGs were predominantly enriched in cellular amino acid catabolic process, response to external biotic stimulus, regulation of the response to salt stress, reactive oxygen species (ROS) biosynthetic process, regulation of response to osmotic stress, ect. The DEMs were mostly associated with amino acid metabolism, carbohydrate metabolism, phenylalanine metabolism, carbapenem biosynthesis, and pantothenate and CoA biosynthesis. Further analysis identified some critical genes (gene involved in the oxidative stress response, gene encoding transcription factor (TF) and gene involved in the synthesis of metabolite such as alanine, asparagine, aspartate, glutamate, glutamine, 4-aminobutyric acid, abscisic acid, jasmonic acid, ect.) that potentially participated in a complex regulatory network in the wheat response to NaCl stress. The expression of the upregulated DEGs and DEMs were higher, and the expression of the down-regulated DEGs and DEMs was lower in 3-MA-treated plants under NaCl treatment.

CONCLUSION

3-MA enhanced the salt stress sensitivity of wheat seedlings by inhibiting the activity of the roots and leaves, inhibiting autophagy in the roots and leaves, increasing the content of both H₂O₂ and O₂•-, damaged photosynthesis apparatus and changing the transcriptome and metabolome of salt-stressed wheat seedlings.

Anti-obesity effect of Auricularia heimuer fruiting body alcohol extraction on obese mice and crucial metabolite pathway analysis by liquid chromatography-tandem mass spectrometry

In recent years, the increasing obese and overweight population has become a worldwide public health problem, as there is no effective medication to control obesity. Auricularia heimuer is rich in active substances that have potential biologically active functions. The anti-obesity effect and mechanism of Auricularia heimuer fruiting body alcohol extraction (AHA, 150-600 mg/kg·bw) was investigated in obese mice by assessing changes in endogenous liver metabolites using a liquid chromatography-tandem mass spectrometry approach. The aim of this study was to identify an effective food to control human obesity. AHA of 600 mg/kg·bw (HC) significantly decreased body weight and improved serum biochemistry indices. Sixty-eight liver metabolites were identified and significantly separated among the normal, high-fat diet (HFD), and HC groups. Moreover, the metabolic analysis revealed that HC significantly regulated specific metabolites in mice including amino acids, lipids, and carbohydrate compounds. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that HC was significantly involved in different metabolite pathways including arachidonic acid metabolism, galactose metabolism, carbohydrate digestion and absorption, linoleic acid metabolism, and starch and sucrose metabolism. Eight weeks after supplementing with HC, major metabolites in related pathways that were disrupted by an HFD were restored to normal levels, suggesting that HC had anti-obesity activity.

Combined transcriptome and metabolome integrated analysis of Acer mandshuricum to reveal candidate genes involved in anthocyanin accumulation

The red color formation of Acer mandshuricum leaves is caused by the accumulation of anthocyanins primarily, but the molecular mechanism researches which underlie anthocyanin biosynthesis in A. mandshuricum were still lacking. Therefore, we combined the transcriptome and metabolome and analyzed the regulatory mechanism and accumulation pattern of anthocyanins in three different leaf color states. In our results, 26 anthocyanins were identified. Notably, the metabolite cyanidin 3-O-glucoside was found that significantly correlated with the color formation, was the predominant metabolite in anthocyanin biosynthesis of A. mandshuricum. By the way, two key structural genes ANS (Cluster-20561.86285) and BZ1 (Cluster-20561.99238) in anthocyanidin biosynthesis pathway were significantly up-regulated in RL, suggesting that they might enhance accumulation of cyanidin 3-O-glucoside which is their downstream metabolite, and contributed the red formation of A. mandshuricum leaves. Additionally, most TFs (e.g., MYBs, bZIPs and bHLHs) were detected differentially expressed in three leaf color stages that could participate in anthocyanin accumulation. This study sheds light on the anthocyanin molecular regulation of anthocyanidin biosynthesis and accumulation underlying the different leaf color change periods in A. mandshuricum, and it could provide basic theory and new insight for the leaf color related genetic improvement of A. mandshuricum.