Transcriptome and metabolome analysis of stress tolerance to aluminium in Vitis quinquangularis

The grapevine miR827a regulates the synthesis of stilbenes by targeting VqMYB14 and gives rise to susceptibility in plant immunity

Grapevine (Vitis vinifera L.) is an economically important fruit crop cultivated worldwide. In China, grapevine cultivation is very extensive, and a few Vitis grapes have excellent pathogen and stress resistance, but the molecular mechanisms underlying the grapevine response to stress remain unclear. In this study, a microRNA (miRNA; miR827a), which negatively regulates its target gene VqMYB14, a key regulatory role in the synthesis of stilbenes, was identified in Vitis quinquangularis (V. quinquangularis) using transcriptome sequencing. Using overexpression and silencing approaches, we found that miR827a regulates the synthesis of stilbenes by targeting VqMYB14. We used flagellin N-terminal 22-amino-acid peptide (flg22), the representative elicitor in plant basal immunity, as the elicitor to verify whether miR827a is involved in the basal immunity of V. quinquangularis. Furthermore, the promoter activity of miR827a was alleviated in transgenic grape protoplasts and Arabidopsis thaliana following treatment with flg22 and Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000), respectively. In addition, yeast one-hybrid and dual luciferase reporter assay revealed that the ethylene transcription factor VqERF057 acted as a key regulator in the inhibition of miR827a transcription. These results will contribute to the understanding of the biological functions of miR827a in grapevine and clarify the molecular mechanism of the interaction between miR827a and VqMYB14.

Aluminum-Immobilizing Rhizobacteria Modulate Root Exudation and Nutrient Uptake and Increase Aluminum Tolerance of Pea Mutant E107 (brz)

It is well known that plant-growth-promoting rhizobacteria (PGPRs) increase the tolerance of plants to abiotic stresses; however, the counteraction of Al toxicity has received little attention. The effects of specially selected Al-tolerant and Al-immobilizing microorganisms were investigated using pea cultivar Sparkle and its Al-sensitive mutant E107 (brz). The strain Cupriavidus sp. D39 was the most-efficient in the growth promotion of hydroponically grown peas treated with 80 µM AlCl₃, increasing the plant biomass of Sparkle by 20% and of E107 (brz) by two-times. This strain immobilized Al in the nutrient solution and decreased its concentration in E107 (brz) roots. The mutant showed upregulated exudation of organic acids, amino acids, and sugars in the absence or presence of Al as compared with Sparkle, and in most cases, the Al treatment stimulated exudation. Bacteria utilized root exudates and more actively colonized the root surface of E107 (brz). The exudation of tryptophan and the production of IAA by Cupriavidus sp. D39 in the root zone of the Al-treated mutant were observed. Aluminum disturbed the concentrations of nutrients in plants, but inoculation with Cupriavidus sp. D39 partially restored such negative effects. Thus, the E107 (brz) mutant is a useful tool for studying the mechanisms of plant-microbe interactions, and PGPR plays an important role in protecting plants against Al toxicity.

Comprehensive Transcriptomic and Metabolic Profiling of Agrobacterium-tumefaciens-Infected Immature Wheat Embryos

The transformation efficiency (TE) was improved by a series of special chemical and physical methods using immature embryos from the cultivar Fielder, with the PureWheat technique. To analyze the reaction of immature embryos infected, which seemed to provide the necessary by Agrobacterium tumefaciens in PureWheat, a combination of scanning electron microscopy (SEM), complete transcriptome analysis, and metabolome analysis was conducted to understand the progress. The results of the SEM analysis revealed that Agrobacterium tumefaciens were deposited under the damaged cortex of immature embryos as a result of pretreatment and contacted the receptor cells to improve the TE. Transcriptome analysis indicated that the differentially expressed genes were mainly enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, plant-pathogen interaction, plant hormone signal transduction, and the MAPK (Mitogen-activated protein kinase) signaling pathway. By analyzing the correlation between differentially expressed genes and metabolites, the expression of many genes and the accumulation of metabolites were changed in glucose metabolism and the TCA cycle (Citrate cycle), as well as the amino acid metabolism; this suggests that the infection of wheat embryos with Agrobacterium is an energy-demanding process. The shikimate pathway may act as a hub between glucose metabolism and phenylpropanoid metabolism during Agrobacterium infection. The downregulation of the F5H gene and upregulation of the CCR gene led to the accumulation of lignin precursors through phenylpropanoid metabolism. In addition, several metabolic pathways and oxidases were found to be involved in the infection treatment, including melatonin biosynthesis, benzoxazinoid biosynthesis, betaine biosynthesis, superoxide dismutase, and peroxidase, suggesting that wheat embryos may be under the stress of Agrobacterium and, thus, undergo an oxidative stress response. These findings explore the physiological and molecular changes of immature embryos during the co-culture stage of the PureWheat technique and provide insights for Agrobacterium-mediated transgenic wheat experiments.

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.

Molecular mechanisms for pH-mediated amelioration of aluminum-toxicity revealed by conjoint analysis of transcriptome and metabolome in Citrus sinensis roots

Little is known about the effects of pH-aluminum (Al) interactions on gene expression and/or metabolite profiles in plants. Eleven-week-old seedlings of Citrus sinensis were fertilized with nutrient solution at an Al level of 0 or 1 mM and a pH of 3.0 or 4.0 for 18 weeks. Increased pH mitigated Al-toxicity-induced accumulation of callose, an Al-sensitive marker. In this study, we identified more differentially expressed genes and differentially abundant metabolites in pH 4.0 + 1 mM Al-treated roots (P4AR) vs pH 4.0 + 0 mM Al-treated roots (P4R) than in pH 3.0 + 1 mM Al-treated roots (P3AR) vs pH 3.0 + 0 mM Al-treated roots (P3R), suggesting that increased pH enhanced root metabolic adaptations to Al-toxicity. Further analysis indicated that increased pH-mediated mitigation of root Al-toxicity might be related to several factors, including: enhanced capacity to maintain the homeostasis of phosphate and energy and the balance between generation and scavenging of reactive oxygen species and aldehydes; and elevated accumulation of secondary metabolites such as polyphenol, proanthocyanidins and phenolamides and adaptations of cell wall and plasma membrane to Al-toxicity.

ABA Mediates Plant Development and Abiotic Stress via Alternative Splicing

Alternative splicing (AS) exists in eukaryotes to increase the complexity and adaptability of systems under biophysiological conditions by increasing transcriptional and protein diversity. As a classic hormone, abscisic acid (ABA) can effectively control plant growth, improve stress resistance, and promote dormancy. At the transcriptional level, ABA helps plants respond to the outside world by regulating transcription factors through signal transduction pathways to regulate gene expression. However, at the post-transcriptional level, the mechanism by which ABA can regulate plant biological processes by mediating alternative splicing is not well understood. Therefore, this paper briefly introduces the mechanism of ABA-induced alternative splicing and the role of ABA mediating AS in plant response to the environment and its own growth.