MdSnRK1.1 interacts with MdJAZ18 to regulate sucrose-induced anthocyanin and proanthocyanidin accumulation in apple

Metabolomic and transcriptomic analyses of peach leaves and fruits in response to pruning

BACKGROUND

Pruning is an important cultivation management option that has important effects on peach yield and quality. However, the effects of pruning on the overall genetic and metabolic changes in peach leaves and fruits are poorly understood.

RESULTS

The transcriptomic and metabolomic profiles of leaves and fruits from trees subjected to pruning and unpruning treatments were measured. A total of 20,633 genes and 622 metabolites were detected. Compared with those in the control, 1,127 differentially expressed genes (DEGs) and 77 differentially expressed metabolites (DEMs) were identified in leaves from pruned and unpruned trees (pdLvsupdL), whereas 423 DEGs and 29 DEMs were identified in fruits from the pairwise comparison pdFvsupdF. The content of three auxin analogues was upregulated in the leaves of pruned trees, the content of all flavonoids detected in the leaves decreased, and the expression of almost all genes involved in the flavonoid biosynthesis pathway decreased. The phenolic acid and amino acid metabolites detected in fruits from pruned trees were downregulated, and all terpenoids were upregulated. The correlation analysis revealed that DEGs and DEMs in leaves were enriched in tryptophan metabolism, auxin signal transduction, and flavonoid biosynthesis. DEGs and DEMs in fruits were enriched in flavonoid and phenylpropanoid biosynthesis, as well as L-glutamic acid biosynthesis.

CONCLUSIONS

Pruning has different effects on the leaves and fruits of peach trees, affecting mainly the secondary metabolism and hormone signalling pathways in leaves and amino acid biosynthesis in fruits.

Apple SINA11-JAZ2 module is involved in jasmonate signaling response

The E3 ubiquitin ligase MdSINA11 targets the jasmonate ZIM domain protein MdJAZ2 for ubiquitination and degradation through the 26S proteasome pathway, thereby initiating jasmonate signaling and jasmonic acid-triggered anthocyanin biosynthesis in apple.

The critical roles of three sugar-related proteins (HXK, SnRK1, TOR) in regulating plant growth and stress responses

Sugar signaling is one of the most critical regulatory signals in plants, and its metabolic network contains multiple regulatory factors. Sugar signal molecules regulate cellular activities and organism development by combining with other intrinsic regulatory factors and environmental inputs. HXK, SnRK1, and TOR are three fundamental proteins that have a pivotal role in the metabolism of sugars in plants. HXK, being the initial glucose sensor discovered in plants, is renowned for its multifaceted characteristics. Recent investigations have unveiled that HXK additionally assumes a significant role in plant hormonal signaling and abiotic stress. SnRK1 serves as a vital regulator of growth under energy-depleted circumstances, whereas TOR, a large protein, acts as a central integrator of signaling pathways that govern cell metabolism, organ development, and transcriptome reprogramming in response to diverse stimuli. Together, these two proteins work to sense upstream signals and modulate downstream signals to regulate cell growth and proliferation. In recent years, there has been an increasing amount of research on these three proteins, particularly on TOR and SnRK1. Furthermore, studies have found that these three proteins not only regulate sugar signaling but also exhibit certain signal crosstalk in regulating plant growth and development. This review provides a comprehensive overview and summary of the basic functions and regulatory networks of these three proteins. It aims to serve as a reference for further exploration of the interactions between these three proteins and their involvement in co-regulatory networks.

Calmodulin-like protein MdCML15 interacts with MdBT2 to modulate iron homeostasis in apple

BTB and TAZ domain proteins (BTs) function as specialized adaptors facilitating substrate recognition of the CUL3-RING ubiquitin ligase (CRL3) complex that targets proteins for ubiquitination in reaction to diverse pressures. Nonetheless, knowledge of the molecular mechanisms by which the apple scaffold protein MdBT2 responds to external and internal signals is limited. Here we demonstrate that a putative Ca 2+ sensor, calmodulin-like 15 (MdCML15), acts as an upstream regulator of MdBT2 to negatively modulate its functions in plasma membrane H+-ATPase regulation and iron deficiency tolerance. MdCML15 was identified to be substantially linked to MdBT2, and to result in the ubiquitination and degradation of the MdBT2 target protein MdbHLH104. Consequently, MdCML15 repressed the MdbHLH104 target, MdAHA8's expression, reducing levels of a specific membrane H+-ATPase. Finally, the phenotype of transgenic apple plantlets and calli demonstrated that MdCML15 modulates membrane H+-ATPase-produced rhizosphere pH lowering alongside iron homeostasis through an MdCML15-MdBT2-MdbHLH104-MdAHA8 pathway. Our results provide new insights into the relationship between Ca2+ signaling and iron homeostasis.

Integrated transcriptomic and metabolomic analyses elucidate the mechanism of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress

Seed propagation is the main method of mulberry expansion in China, an important economic forest species. However, seed germination is the most sensitive stage to various abiotic stresses, especially salinity stress. To reveal the molecular regulatory mechanism of mulberry seed germination under salt stress, flavonoid metabolomics and transcriptomics analyses were performed on mulberry seeds germinated under 50 and 100 mmol/L NaCl stress. Analysis of the flavonoid metabolome revealed that a total of 145 differential flavonoid metabolites (DFMs) were classified into 9 groups, 40 flavonols, 32 flavones, 16 chalcones and 14 flavanones. Among them, 61.4% (89) of the DFMs accumulated continuously with increasing salt concentration, reaching the highest level at a 100 mmol/L salt concentration; these DFMs included quercetin-3-O-glucoside (isoquercitrin), kaempferol (3,5,7,4'-tetrahydroxyflavone), quercetin-7-O-glucoside, taxifolin (dihydroquercetin) and apigenin (4',5,7-trihydroxyflavone), indicating that these flavonoids may be key metabolites involved in the response to salt stress. Transcriptional analysis identified a total of 3055 differentially expressed genes (DEGs), most of which were enriched in flavonoid biosynthesis (ko00941), phenylpropanoid biosynthesis (ko00940) and biosynthesis of secondary metabolites (ko01110). Combined analysis of flavonoid metabolomic and transcriptomic data indicated that phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), flavonol synthase (FLS), bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR) and anthocyanidin reductase (ANR) were the key genes involved in flavonoid accumulation during mulberry seed germination under 50 and 100 mmol/L NaCl stress. In addition, three transcription factors, MYB, bHLH and NAC, were involved in the regulation of flavonoid accumulation under salt stress. The results of quantitative real-time PCR (qRT‒PCR) validation showed that the expression levels of 11 DEGs, including 7 genes involved in flavonoid biosynthesis, under different salt concentrations were consistent with the transcriptomic data, and parallel reaction monitoring (PRM) results showed that the expression levels of 6 key enzymes (proteins) involved in flavonoid synthesis were consistent with the accumulation of flavonoids. This study provides a new perspective for investigating the regulatory role of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress at different concentrations.

MdSnRK1.1 interacts with MdGLK1 to regulate abscisic acid-mediated chlorophyll accumulation in apple

Abscisic acid (ABA), as a plant hormone, plays a positive role in leaf chlorosis; however, the underlying molecular mechanism is less known. Our findings provide ABA treatment reduced the chlorophyll accumulation in apple, and Malus × domestica Sucrose Non-fermenting 1-Related Protein Kinase 1.1 (MdSnRK1.1) participates in the process. MdSnRK1.1 interacts with MdGLK1, a GOLDEN2-like transcription factor that orchestrates development of the chloroplast. Furthermore, MdSnRK1.1 affects MdGLK1 protein stability through phosphorylation. We found that Ser468 of MdGLK1 is target site of MdSnRK1.1 phosphorylation. MdSnRK1.1-mediated phosphorylation was critical for MdGLK1 binding to the target gene MdHEMA1 promoters. Collectively, our results demonstrate that ABA activates MdSnRK1.1 to degrade MdGLK1 and inhibit the accumulation of chlorophyll. These findings extend our understanding on how MdSnRK1.1 balances normal growth and hormone response.

Spraying phenolic acid-modifiedchitooligosaccharide derivatives improves anthocyanin accumulation in grape

Herein, four chitooligosaccharide derivatives (COS-RA, COS-FA, COS-VA, COS-GA) were prepared by laccase-catalyzed chitooligosaccharide modification with rosmarinic acid (RA), ferulic acid (FA), gallic acid (GA), and vanillic acid (VA), and structures were characterized. RA and FA resulted in higher amino-substitution in the chitooligosaccharides than GA and VA. COS-RA and COS-FA had greater DPPH scavenging rates than COS-GA and COS-VA. Compared with COS treatment, spraying 250 mg L-1 COS-RA or COS-VA 6 times (once per 7 days) increased soluble sugar and anthocyanin content by 18.6%-23.2% and 41.7%-46.7%, respectively, from the fruit expansion to harvest stage. COS-RA and COS-VA also enhanced gene expression related to anthocyanin synthesis (PAL, F3H, F3'5'H, DFR, and UFGT) and monomeric anthocyanin accumulation (Mal-3-O-glu, Petu-3-O-ace-glu, Del-3-O-glu). Therefore, chitooligosaccharide derivatives may improve grape fruit anthocyanin accumulation by regulating antioxidant systems, improving the photosynthetic rate and inducing gene expression related to anthocyanin synthesis.

Genome-Wide Analysis of the bHLH Gene Family in Loropetalum chinense var. rubrum: Identification, Classification, Evolution, and Diversity of Expression Patterns under Cultivation

The basic helix-loop-helix (bHLH) transcription factor family is the second-largest transcription factor family in plants. Members of this family are involved in the processes of growth and development, secondary metabolic biosynthesis, signal transduction, and plant resistance. Loropetalum chinense var. rubrum is a critical woody plant with higher ornamental and economic values, which has been used as ornamental architecture and traditional Chinese herbal medicine plants. However, the bHLH transcription factors in Loropetalum chinense var. rubrum (L. chinense var. rubrum) have not yet been systematically demonstrated, and their role in the biosynthesis of anthocyanin is still unclear. Here, we identified 165 potential LcbHLHs genes by using two methods, and they were unequally distributed on chromosomes 1 to 12 of the genome of L. chinense var. rubrum. Based on an evolutionary comparison with proteins from Arabidopsis and Oryza sativa, these bHLH proteins were categorized into 21 subfamilies. Most LcbHLHs in a particular subfamily had similar gene structures and conserved motifs. The Gene Ontology annotation and Cis-elements predicted that LcbHLHs had many molecular functions and were involved in processes of plant growth, including the biosynthesis of flavonoids and anthocyanins. Transcriptomic analysis revealed different expression patterns among different tissues and cultivars of L. chinense var. rubrum. Many LcbHLHs were expressed in the leaves, and only a few genes were highly expressed in the flowers. Six LcbHLHs candidate genes were identified by bioinformatics analysis and expression analysis. Further Real-time quantitative PCR analysis and protein interaction network analysis showed that LcbHLH156, which is one of the candidate proteins belonging to the IIIf subfamily, could interact with proteins related to anthocyanin synthesis. Therefore, LcbHLH156 was transiently expressed in L. chinense var. rubrum to verify its function in regulating anthocyanin synthesis. Compared with the control group, red pigment accumulation appeared at the wound after injection, and the total anthocyanin content increased at the wound of leaves. These results lay a foundation for the research of the regulation mechanism of leaf colors in L. chinense var. rubrum and also provide a basis for the function of the LcbHLH family.

Effect of sucrose as an elicitor in increasing quercetin-3-O-rhamnoside (quercitrin) content of chrysanthemum (Chrysanthemum morifolium Ramat) callus culture based on harvest time differences

Chrysanthemum (Chrysanthemum morifolium) contains secondary metabolites, such as flavonoid compounds, especially luteolin-7-glucoside and quercetin-3-O-rhamnoside (quercitrin), in its tissues. Utilizing sucrose as an elicitor through callus culture presents an alternative method to enhance the production of secondary metabolites. This research aimed to determine the best sucrose concentration and harvest time for maximizing quercitrin content in chrysanthemum callus culture. The research employed a completely randomized design with four treatment groups: 0, 30, 45, and 60 g/l of sucrose added to MS medium containing 4 ppm 2,4-dichlorophenoxyacetic acid (2,4-D). Callus samples were harvested on the 15th and 30th days of culture. The observed parameters included callus morphology (color and texture), fresh weight, dry weight, the diameter of the callus, and quercitrin content analyzed using high-performance liquid chromatography. The results showed that all callus cultures exhibited intermediate textures and varied colors, predominantly shades of brown. The treatment involving 45 g/l of sucrose with a 30th-day harvest yielded the highest fresh weight, dry weight, and quercitrin content, namely 2.108 g, 0.051 g, and 0.437 mg/g DW, respectively. Notably, the quercitrin content exhibited a 63.67% increase compared to the control.

The CALCINEURIN B-LIKE 4/CBL-INTERACTING PROTEIN 3 module degrades repressor JAZ5 during rose petal senescence

Flower senescence is genetically regulated and developmentally controlled. The phytohormone ethylene induces flower senescence in rose (Rosa hybrida), but the underlying signaling network is not well understood. Given that calcium regulates senescence in animals and plants, we explored the role of calcium in petal senescence. Here, we report that the expression of calcineurin B-like protein 4 (RhCBL4), which encodes a calcium receptor, is induced by senescence and ethylene signaling in rose petals. RhCBL4 interacts with CBL-interacting protein kinase 3 (RhCIPK3), and both positively regulate petal senescence. Furthermore, we determined that RhCIPK3 interacts with the jasmonic acid response repressor jasmonate ZIM-domain 5 (RhJAZ5). RhCIPK3 phosphorylates RhJAZ5 and promotes its degradation in the presence of ethylene. Our results reveal that the RhCBL4-RhCIPK3-RhJAZ5 module mediates ethylene-regulated petal senescence. These findings provide insights into flower senescence, which may facilitate innovations in postharvest technology for extending rose flower longevity.

SnRK1 inhibits anthocyanin biosynthesis through both transcriptional regulation and direct phosphorylation and dissociation of the MYB/bHLH/TTG1 MBW complex

Plants have evolved an extensive specialized secondary metabolism. The colorful flavonoid anthocyanins, for example, not only stimulate flower pollination and seed dispersal, but also protect different tissues against high light, UV and oxidative stress. Their biosynthesis is highly regulated by environmental and developmental cues and induced by high sucrose levels. Expression of the biosynthetic enzymes involved is controlled by a transcriptional MBW complex, comprising (R2R3) MYB- and bHLH-type transcription factors and the WD40 repeat protein TTG1. Anthocyanin biosynthesis is not only useful, but also carbon- and energy-intensive and non-vital. Consistently, the SnRK1 protein kinase, a metabolic sensor activated in carbon- and energy-depleting stress conditions, represses anthocyanin biosynthesis. Here we show that Arabidopsis SnRK1 represses MBW complex activity both at the transcriptional and post-translational level. In addition to repressing expression of the key transcription factor MYB75/PAP1, SnRK1 activity triggers MBW complex dissociation, associated with loss of target promoter binding, MYB75 protein degradation and nuclear export of TTG1. We also provide evidence for direct interaction with and phosphorylation of multiple MBW complex proteins. These results indicate that repression of expensive anthocyanin biosynthesis is an important strategy to save energy and redirect carbon flow to more essential processes for survival in metabolic stress conditions.

A Soybean Sucrose Non-Fermenting Protein Kinase 1 Gene, GmSNF1, Positively Regulates Plant Response to Salt and Salt-Alkali Stress in Transgenic Plants

Soybean is one of the most widely grown oilseed crops worldwide. Several unfavorable factors, including salt and salt-alkali stress caused by soil salinization, affect soybean yield and quality. Therefore, exploring the molecular basis of salt tolerance in plants and developing genetic resources for genetic breeding is important. Sucrose non-fermentable protein kinase 1 (SnRK1) belongs to a class of Ser/Thr protein kinases that are evolutionarily highly conserved direct homologs of yeast SNF1 and animal AMPKs and are involved in various abiotic stresses in plants. The GmPKS4 gene was experimentally shown to be involved with salinity tolerance. First, using the yeast two-hybrid technique and bimolecular fluorescence complementation (BiFC) technique, the GmSNF1 protein was shown to interact with the GmPKS4 protein. Second, the GmSNF1 gene responded positively to salt and salt-alkali stress according to qRT-PCR analysis, and the GmSNF1 protein was localized in the nucleus and cytoplasm using subcellular localization assay. The GmSNF1 gene was then heterologously expressed in yeast, and the GmSNF1 gene was tentatively identified as having salt and salt-alkali tolerance function. Finally, the salt-alkali tolerance function of the GmSNF1 gene was demonstrated by transgenic Arabidopsis thaliana, soybean hairy root complex plants overexpressing GmSNF1 and GmSNF1 gene-silenced soybean using VIGS. These results indicated that GmSNF1 might be useful in genetic engineering to improve plant salt and salt-alkali tolerance.

Why do plants blush when they are hungry?

Foliar anthocyanins, as well as other secondary metabolites, accumulate transiently under nutritional stress. A misconception that only nitrogen or phosphorus deficiency induces leaf purpling/reddening has led to overuse of fertilizers that burden the environment. Here, we emphasize that several other nutritional imbalances induce anthocyanin accumulation, and nutrient-specific differences in this response have been reported for some deficiencies. A range of ecophysiological functions have been attributed to anthocyanins. We discuss the proposed functions and signalling pathways that elicit anthocyanin synthesis in nutrient-stressed leaves. Knowledge from the fields of genetics, molecular biology, ecophysiology and plant nutrition is combined to deduce how and why anthocyanins accumulate under nutritional stress. Future research to fully understand the mechanisms and nuances of foliar anthocyanin accumulation in nutrient-stressed crops could be utilized to allow these leaf pigments to act as bioindicators for demand-oriented application of fertilizers. This would benefit the environment, being timely due to the increasing impact of the climate crisis on crop performance.

Anthocyanins distribution, transcriptional regulation, epigenetic and post-translational modification in fruits

Anthocyanins have indispensable functions in plant resistance, human health, and fruit coloring, which arouse people's favorite. It has been reported that anthocyanins are widely found in fruits, and can be affected by numerous factors. In this review, we systematically summarize anthocyanin functions, classifications, distributions, biosynthesis, decoration, transportation, transcriptional regulation, DNA methylation, and post-translational regulation in fruits.

Comprehensive metabolomics-based analysis of sugar composition and content in berries of 18 grape varieties

Xinjiang is the largest grape-producing region in China and the main grape cultivation area in the world. The Eurasian grape resources grown in Xinjiang are very rich in diversity. The sugar composition and content are the main factors that determine the quality of berries. However, there are currently no systematic reports on the types and contents of sugars in grapes grown in Xinjiang region. In this research, we evaluated the appearance and fruit maturity indicators of 18 grape varieties during fruit ripening and determined their sugar content using GC-MS. All cultivars primarily contained glucose, D-fructose, and sucrose. The glucose content in varieties varied from 42.13% to 46.80% of the total sugar, whereas the fructose and sucrose contents varied from 42.68% to 50.95% and 6.17% to 12.69%, respectively. The content of trace sugar identified in grape varieties varied from 0.6 to 2.3 mg/g. The comprehensive assessment by principal component analysis revealed strong positive correlations between some sugar components. A comprehensive study on the content and types of sugar will provide the foundation to determine the quality of grape cultivars and effective ways to utilize resources to improve sugar content through breeding.

A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis

Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.

FtbZIP85 Is Involved in the Accumulation of Proanthocyanidin by Regulating the Transcription of FtDFR in Tartary Buckwheat

As a drought-tolerant crop, Tartary buckwheat survives under adverse environmental conditions, including drought stress. Proanthocyanidins (PAs) and anthocyanins are flavonoid compounds, and they participate in the regulation of resistance to both biotic and abiotic stresses by triggering genes' biosynthesis of flavonoids. In this study, a basic leucine zipper, basic leucine zipper 85 (FtbZIP85), which was predominantly expressed in seeds, was isolated from Tartary buckwheat. Our study shows that the expressions of FtDFR, FtbZIP85 and FtSnRK2.6 were tissue-specific and located in both the nucleus and the cytosol. FtbZIP85 could positively regulate PA biosynthesis by binding to the ABA-responsive element (ABRE) in the promoter of dihydroflavonol 4-reductase (FtDFR), which is a key enzyme in the phenylpropanoid biosynthetic pathway. Additionally, FtbZIP85 was also involved in the regulation of PA biosynthesis via interactions with FtSnRK2.6 but not with FtSnRK2.2/2.3. This study reveals that FtbZIP85 is a positive regulator of PA biosynthesis in TB.

The complexities of proanthocyanidin biosynthesis and its regulation in plants

Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.

VaSUS2 confers cold tolerance in transgenic tomato and Arabidopsis by regulation of sucrose metabolism and ROS homeostasis

VaSUS2 enhances cold tolerance of transgenic tomato and Arabidopsis by regulating sucrose metabolism and improving antioxidant enzymes activity. Sucrose synthetase (SUS) is a key enzyme of sugar metabolism, and plays an important role in response to abiotic stress in plant. However, the function of VaSUS2 remains unknown in cold tolerance. Here, the cloning and functional characterization of the plasma membrane-localized VaSUS2 gene isolated from Vitis amurensis was studied. The transcript level of VaSUS2 was up-regulated under cold stress in Vitis amurensis. Heterologous expression of VaSUS2 in tomato increased SUS activity, which promoted the accumulation of glucose and fructose under cold treatment. The transgenic tomato and Arabidopsis exhibited higher levels of antioxidant enzymes activity, lower relative electrolyte leakage (REL), malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) content compared to wild type under cold stress. Importantly, the ability of scavenging reactive oxygen species (ROS) in transgenic plants was significantly improved. Moreover, yeast two-hybrid (Y2H) indicated that VaSnRK1 might be a potential interaction protein of VaSUS2. qRT-PCR showed that sucrose metabolism-related genes SlSUS, SlSPS and SlINV were significantly up-regulated in transgenic tomatoes. Meanwhile, the expression levels of antioxidant enzyme genes and cold-related genes CBF1, COR47 and ICE1 were up-regulated in transgenic plants. Taken together, these results suggested that VaSUS2 was involved in cold tolerance by increasing the levels of soluble sugars, improving the activity of antioxidant enzymes, and up-regulating the expression of cold-related genes in transgenic tomatoes and Arabidopsis.

Functional characterization of MdERF113 in apple

The AP2/ERF family is an important class of transcription factors involved in plant growth and various biological processes. One of the AP2/ERF transcription factors, RAP2.6L, participates in various stresses responses. However, the function of RAP2.6L is largely unknown in apples (Malus domestica). In this study, an apple gene homologous to Arabidopsis AtRAP2.6L, MdERF113, was analyzed by bioinformatic characterization, gene expression analysis and subcellular localization assessment. MdERF113 was highly expressed in the sarcocarp and was responsive to hormonal signals and abiotic stresses. MdERF113-overexpression apple calli were less sensitive to low temperature, drought, salinity, and abscisic acid than wild-type. Subcellular localization revealed that MdERF113 was a nuclear-localized transcription factor, and yeast experiments confirmed that MdERF113 has no autonomous activation activity. Overall, this study indicated that MdERF113 plays a role in regulating plant growth under abiotic conditions.

VvTOR interacts with VvSnRK1.1 and regulates sugar metabolism in grape

VvTOR interacts with VvSnRK1.1 and regulates sugar accumulation and sugar-related genes expression in grape. Target of rapamycin (TOR) and sucrose-non-fermenting-related protein kinase 1.1 (SnRK1.1) both are critical proteins in plant sugar metabolism. Glucose-TOR signaling dictates transcriptional reprogramming of gene sets involved in central and secondary metabolism, cell cycle, transcription, signaling, transport and folding. SnRK1.1 is involved in sucrose-induced hypocotyl elongation. However, the relationship of TOR and SnRK1.1 in regulating sugar metabolism is unclear. In the study, we utilized grape (Vitis vinifera) calli to explore the relationship between TOR and SnRK1.1 in the sugar metabolism. We found that VvTOR interacted with VvSnRK1.1. By subcellular localization, VvTOR was found in the nucleus and cell membrane. Transgenic grape calli achieved by Agrobacterium-mediated transformation contained less glucose compared to WT calli. The fructose contents were markedly increased in the overexpressing VvTOR (OE-VvTOR), OE-VvTOR + RNAi-VvSnRK1.1 and RNAi-VvTOR + OE-VvSnRK1.1 transgenic calli. Sucrose contents were significantly increased in the OE-VvTOR transgenic calli and reduced in the OE-VvTOR + RNAi-VvSnRK1.1 transgenic calli, which implied that the pathway of VvTOR improving sucrose content might need the expression of VvSnRK1.1. VvTOR interacted with VvSnRK1.1 and regulated sugar metabolism in grape. These results suggest that there is a crosstalk between TOR and SnRK1.1 in plant sugar metabolism.

MAPKK2/4/5/7-MAPK3-JAZs modulate phenolic acid biosynthesis in Salvia miltiorrhiza

Phenolic acids are the major bioactive metabolites produced in Salvia miltiorrhiza, a traditional Chinese medicine called Danshen. Many phytohormone elicitor treatments induce phenolic acid biosynthesis, even though the underlying mechanism remains obscure. Expression pattern analysis showed that SmMAPK3 was highly expressed in leaves, and SmMAPK3 was significantly induced by salicylic acid (SA) and methyl jasmonate (JA). Bioinformatics analysis revealed that SmMAPK3 belongs to group A and contains a TEY motif in the activation loop together with three conserved regions (P-loop, C-loop and CD-domain). A previous study speculated that SmMAPK3 is likely a positive regulator in the biosynthesis of phenolic acids in S. miltiorrhiza. In this study, overexpression of SmMAPK3 increased phenolic acid biosynthetic gene expression and enhanced the accumulation of phenolic acids in S. miltiorrhiza plantlets. Yeast two-hybrid (Y2H) analysis and firefly luciferase complementation imaging (LCI) assays revealed that SmMAPKK2/4/5/7-SmMAPK3-SmJAZs form a cascade that regulates the accumulation of phenolic acids. In summary, this work deepens our understanding of the posttranscriptional regulatory mechanisms of phenolic acid biosynthesis and sheds new light on metabolic engineering in S. miltiorrhiza.

Melatonin triggers tissue-specific changes in anthocyanin and hormonal contents during postharvest decay of Angeleno plums

Plum is a stone fruit that stands out for having a short shelf-life because of its high susceptibility to rapid deterioration. Part of this deterioration is explained by fruit overripening. Recently, the role of melatonin in delaying postharvest decay has been investigated but its regulatory function during overripening is still under extensive debate. In this study, to understand physiological events taking place in plums overripening and elucidate the role of melatonin on the postharvest quality of these fruits and its relationship to other plant hormones, Angeleno plums were sprayed with 10^-4 M of melatonin solution immediately after harvest. We carried out tissue-specific (mesocarp and exocarp) analysis of total phenols and anthocyanin quantification, as well as the evaluation of different phytohormones by LC-MS/MS and fruit quality parameters. Results showed that during postharvest, endogenous melatonin contents decreased both in the mesocarp and the exocarp of Angeleno plums. Likewise, plum firmness also decreased and a strong correlation was found for this parameter with jasmonic acid (JA) and cytokinins. Conversely, after exogenous melatonin application, endogenous melatonin content increased both in mesocarp and exocarp but it had a differential effect depending on the plum tissue. Indeed, total phenol and anthocyanin contents arose by 21% and 58%, respectively, in the mesocarp after melatonin treatment but no variations were found in the exocarp of Angeleno plums. Hormonal analysis of Angeleno mesocarp also revealed an increase in the JA and its precursor, 12-oxo-phytodienoic acid (OPDA), on the fourth day after melatonin application as well as a positive correlation between melatonin and gibberellin 1 (GA₁). These results suggest that melatonin may be acting as a signal molecule increasing phenolic compounds contents through direct regulation and by signaling with other phytohormones. Therefore, this research provides valuable information for understanding the regulatory role of melatonin and its relationship with plant hormones during overripening to contribute to improve the postharvest quality of plums.

MdERF1B-MdMYC2 module integrates ethylene and jasmonic acid to regulate the biosynthesis of anthocyanin in apple

Ethylene and jasmonic acid (JA) are crucial hormones that promote anthocyanin synthesis in apple (Malus × domestica). However, the mechanism by which these hormones cooperate to modulate anthocyanin production in apple is unclear. According to our results, MdERF1B expression was strongly induced by ethylene and JA. Physiological phenotypes and the results of molecular biological analyses indicated that MdERF1B encodes a positive regulator of anthocyanin synthesis. Specifically, MdERF1B was capable of combining directly with the MdMYC2 promoter to promote gene expression. Additionally, MdERF1B interacted with two JA signaling pathway inhibitors, namely MdJAZ5 and MdJAZ10. The MdERF1B-MdJAZ5/10 protein complex decreased the ability of MdERF1B to activate the MdMYC2 promoter. Furthermore, MdEIL1, which is a crucial protein for ethylene signal transduction, was observed to bind directly to the MdERF1B promoter, thereby upregulating gene expression. These results suggest that MdERF1B is a core gene responsive to JA and ethylene signals. The encoded protein, together with MdMYC2, MdJAZ5/10, and MdEIL1, modulates anthocyanin synthesis in apple. This study clarifies the synergistic mechanism by which JA and ethylene regulate anthocyanin production in apple.

Regulation of Plant Tannin Synthesis in Crop Species

Plant tannins belong to the antioxidant compound family, which includes chemicals responsible for protecting biological structures from the harmful effects of oxidative stress. A wide range of plants and crops are rich in antioxidant compounds, offering resistance to biotic, mainly against pathogens and herbivores, and abiotic stresses, such as light and wound stresses. These compounds are also related to human health benefits, offering protective effects against cardiovascular and neurodegenerative diseases in addition to providing anti-tumor, anti-inflammatory, and anti-bacterial characteristics. Most of these compounds are structurally and biosynthetically related, being synthesized through the shikimate-phenylpropanoid pathways, offering several classes of plant antioxidants: flavonoids, anthocyanins, and tannins. Tannins are divided into two major classes: condensed tannins or proanthocyanidins and hydrolysable tannins. Hydrolysable tannin synthesis branches directly from the shikimate pathway, while condensed tannins are derived from the flavonoid pathway, one of the branches of the phenylpropanoid pathway. Both types of tannins have been proposed as important molecules for taste perception of many fruits and beverages, especially wine, besides their well-known roles in plant defense and human health. Regulation at the gene level, biosynthesis and degradation have been extensively studied in condensed tannins in crops like grapevine (Vitis vinifera), persimmon (Diospyros kaki) and several berry species due to their high tannin content and their importance in the food and beverage industry. On the other hand, much less information is available regarding hydrolysable tannins, although some key aspects of their biosynthesis and regulation have been recently discovered. Here, we review recent findings about tannin metabolism, information that could be of high importance for crop breeding programs to obtain varieties with enhanced nutritional characteristics.

Molecular components associated with the regulation of flavonoid biosynthesis

Flavonoids exhibit amazing structural diversity and play different roles in plants. Besides, these compounds have been associated with several health benefits in humans. Several exogenous and endogenous cues, for example, light, temperature, nutrient status, and phytohormones have been reported as modulators of biosynthesis and accumulation of flavonoids. Thus, multiple hormones and stress-related signaling pathways are involved in the regulation of gene expression associated with this pathway. The transcriptional regulators belonging to the MYB and bHLH family transcription factors are well documented as the direct regulators of the structural genes associated with flavonoid biosynthesis. Recent studies also suggest that some of these factors are regulated by molecular components involved in stress and hormone signaling pathways. Adapter proteins for transcriptional activation or repression via recruitment of co-activators and co-repressors, respectively, E2 ubiquitin ligases, miRNA processing complex, and DNA methylation/demethylation factors have been recently discovered in various plants to play key roles in fine-tuning flavonoids synthesis. In the present review, we aim to provide comprehensive information about the role of different factors in the regulation of flavonoid biosynthesis. Besides, we describe the potential upstream regulators involved in the regulation of flavonoid biosynthesis within the context of available information. To sum up, the present review furnishes an updated account of signal transduction pathways modulating the biosynthesis of flavonoids.

Sugar signal mediates flavonoid biosynthesis in tea leaves

Sugar metabolism and flavonoid biosynthesis vary with the development of tea leaves. In order to understand the regulatory mechanisms underlying the associations between them, a comprehensive transcriptomic analysis of naturally growing tea leaves at different stages of maturity was carried out. Based on weighted gene coexpression network analysis, the key gene modules (Modules 2 and 3) related to the varying relationship between sugar metabolism and flavonoid biosynthesis as well as the corresponding hub genes were obtained. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that the transcription factors (TFs) in Modules 2 and 3 were mainly enriched in the pathway of plant hormone signal transduction. An in vitro study showed that the transcriptional levels of ERF1B-like TF for hexokinase inhibitor and sucrose treatments were upregulated, being respectively 28.1- and 30.2-fold higher than in the control, suggesting that ERF1B-like TFs participate in the sugar-induced regulation of flavonoid biosynthesis. The results of yeast one-hybrid and dual-luciferase assays demonstrated that CsF3'H, encoding flavonoid 3'-hydroxylase, was the target flavonoid biosynthetic gene for CsERF1B-like TF. Our study identified the potential key regulators participating in the metabolism of sugars and flavonoids, providing new insights into the crosstalk between sugar metabolism and flavonoid biosynthesis in tea plants.

Two MYB and Three bHLH Family Genes Participate in Anthocyanin Accumulation in the Flesh of Peach Fruit Treated with Glucose, Sucrose, Sorbitol, and Fructose In Vitro

Anthocyanins are important pigments in peach fruit and are beneficial to human health. Sugars are both energy-storing and signaling molecules and their roles in inducing anthocyanin biosynthesis have received a great deal of research attention. However, the mechanism by which sugars induce anthocyanin biosynthesis in peach fruit is unknown. In order to understand this induction mechanism, comprehensive transcriptome and metabolome were performed in fruit flesh treated with four different sugars for 12 and 24 h, respectively. Here, we found that cyanidin-3-O-(6-O-p-coumaroyl) glucosides accumulated in fruit flesh treated with glucose, sucrose, sorbitol, and fructose in vitro. Two key structural genes of the anthocyanin biosynthesis pathway, namely, PpDFR and PpUFGT, were upregulated in the flesh of sugar-treated peach fruit. By contrast, the two main transcription factors (TFs) PpMYB10.1 and PpBL regulating anthocyanin biosynthetic genes in peach fruit were not upregulated accordingly. Interestingly, two MYB family genes (PpMYB6 and PpMYB44-like) and three bHLH family genes (PpbHLH35, PpbHLH51, and PpbHLH36-like) were upregulated. A dual luciferase assay revealed that PpMYB6 strongly activated the PpUFGT promoter when it was co-infiltrated with PpbHLH35, PpbHLH51, and PpbHLH36-like. When PpMYB44-like was co-infiltrated with PpbHLH35, it also potently activated the PpUFGT promoter. The results of this study help clarify the molecular mechanisms by which glucose, sucrose, sorbitol, and fructose regulate anthocyanin accumulation in peach fruit.

Construction of yeast one-hybrid library and screening of transcription factors regulating LhMYBSPLATTER expression in Asiatic hybrid lilies (Lilium spp.)

BACKGROUND

Anthocyanins, which belong to flavonoids, are widely colored among red-purple pigments in the Asiatic hybrid lilies (Lilium spp.). Transcription factor (TF) LhMYBSPLATTER (formerly known as LhMYB12-Lat), identified as the major kernel protein, regulating the anthocyanin biosynthesis pathway in 'Tiny Padhye' of Tango Series cultivars, which the pigmentation density is high in the lower half of tepals and this patterning is of exceptional ornamental value. However, the research on mechanism of regulating the spatial and temporal expression differences of LhMYBSPLATTER, which belongs to the R2R3-MYB subfamily, is still not well established. To explore the molecular mechanism of directly related regulatory proteins of LhMYBSPLATTER in the anthocyanin pigmentation, the yeast one-hybrid (Y1H) cDNA library was constructed and characterized.

RESULTS

In this study, we describe a yeast one-hybrid library to screen transcription factors that regulate LhMYBSPLATTER gene expression in Lilium, with the library recombinant efficiency of over 98%. The lengths of inserted fragments ranged from 400 to 2000 bp, and the library capacity reached 1.6 × 10⁶ CFU of cDNA insert, which is suitable to fulfill subsequent screening. Finally, seven prey proteins, including BTF3, MYB4, IAA6-like, ERF4, ARR1, ERF WIN1-like, and ERF061 were screened by the recombinant bait plasmid and verified by interaction with the LhMYBSPLATTER promoter. Among them, ERFs, AUX/IAA, and BTF3 may participate in the negative regulation of the anthocyanin biosynthesis pathway in Lilium.

CONCLUSION

A yeast one-hybrid library of lily was successfully constructed in the tepals for the first time. Seven candidate TFs of LhMYBSPLATTER were screened, which may provide a theoretical basis for the study of floral pigmentation.

The PyPIF5-PymiR156a-PySPL9-PyMYB114/MYB10 module regulates light-induced anthocyanin biosynthesis in red pear

Some cultivars of pear (Pyrus L.) show attractive red fruit skin due to anthocyanin accumulation. This pigmentation can be affected by environmental conditions, especially light. To explore the light-induced regulation network for anthocyanin biosynthesis and fruit coloration in pear, small RNA libraries and mRNA libraries from fruit skins of 'Yunhongyihao' pear were constructed to compare the difference between bagging and debagging treatments. Analysis of RNA-seq of fruit skins with limited light (bagged) and exposed to light (debagged), showed that PyPIF5 was down-regulated after bag removal. PymiR156a was also differentially expressed between bagged and debagged fruit skins. We found that PyPIF5 negatively regulated PymiR156a expression in bagged fruits by directly binding to the G-box motif in its promoter. In addition, PymiR156a overexpression promoted anthocyanin accumulation in both pear skin and apple calli. We confirmed that PymiR156a mediated the cleavage of PySPL9, and that the target PySPL9 protein could form heterodimers with two key anthocyanin regulators (PyMYB114/PyMYB10). We proposed a new module of PyPIF5-PymiR156a-PySPL9-PyMYB114/MYB10. When the bagged fruits were re-exposed to light, PyPIF5 was down-regulated and its inhibitory effect on PymiR156a was weakened, which leads to degradation of the target PySPL, thus eliminating the blocking effect of PySPL on the formation of the regulatory MYB complexes. Ultimately, this promotes anthocyanin biosynthesis in pear skin.

Review: The effects of hormones and environmental factors on anthocyanin biosynthesis in apple

Fruit coloration is an appearance trait that directly affects the commercial value and market competitiveness of apples. The red color of apple fruit is mainly affected by anthocyanin accumulation, and the synthesis of anthocyanin is affected by various factors. The critical roles of hormones and environmental factors during apple anthocyanin biosynthesis are described. This review also elaborates the specific mechanisms of the responses of internal genes to stress and changes in anthocyanin when apples are exposed to different environmental stressors. This study provides direction for future research on apple anthocyanin and is a reference for anthocyanin studies in other species.

Insights into the effect of human civilization on Malus evolution and domestication

The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA-like gene that underwent selection during domestication on 15^th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB-ARC domain-containing gene was found to strongly affect anthocyanin accumulation using a genome-wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.

Abscisic acid receptors are involves in the Jasmonate signaling in Arabidopsis

The phytohormones jasmonates (JAs) act as important molecules of elicitors for the chlorophyll degradation and anthocyanin biosynthesis. JAs do usually not act independently but integrate in complex networks linking to other hormonal signaling transduction. Here, the crosstalk was detected between the JAs (jasmonic acid) and abscisic acid (ABA) signaling pathways in the mediation of chlorophyll degradation and anthocyanin biosynthesis. In this study, we found that the ABA receptor mutants, pyr1pyl1pyl2pyl4 (1124) and pyr1pyl1ply2pyl4pyl5pyl8 (112458) showed less level of chlorophyll and anthocyanin than the wild-type plants, while gain-of-function of RCAR13 transgenic lines inhibited chlorophyll degradation and enhanced anthocyanin accumulation after MeJA treatment. The amidohydrolases, including ILL6 and IAR3 and cytochrome P450 (CYP94B3), encoding JA-Ile catabolism were markedly depressed by ABA receptors. While transcripts of the enzymes for activation of anthocyanin biosynthesis pathway were analyzed, the results indicating that JA biosynthetic genes, including allene oxide synthase (AOS), LOX3 and LOX4 were enhanced by the link of JAs and ABA receptors. Moreover, the ABA receptors are also involved in JAs signal transduction through the regulation of COI, JAZ and MYC2 transcripts. These findings elucidate a connection between a core component of the ABA signaling pathway and JA responses.

BIN2 negatively regulates plant defence against Verticillium dahliae in Arabidopsis and cotton

Verticillium wilt is caused by the soil-borne vascular pathogen Verticillium dahliae, and affects a wide range of economically important crops, including upland cotton (Gossypium hirsutum). Previous studies showed that expression levels of BIN2 were significantly down-regulated during infestation with V. dahliae. However, the underlying molecular mechanism of BIN2 in plant regulation against V. dahliae remains enigmatic. Here, we characterized a protein kinase GhBIN2 from Gossypium hirsutum, and identified GhBIN2 as a negative regulator of resistance to V. dahliae. The Verticillium wilt resistance of Arabidopsis and cotton were significantly enhanced when BIN2 was knocked down. Constitutive expression of BIN2 attenuated plant resistance to V. dahliae. We found that BIN2 regulated plant endogenous JA content and influenced the expression of JA-responsive marker genes. Further analysis revealed that BIN2 interacted with and phosphorylated JAZ family proteins, key repressors of the JA signalling pathway in both Arabidopsis and cotton. Spectrometric analysis and site-directed mutagenesis showed that BIN2 phosphorylated AtJAZ1 at T196, resulting in the degradation of JAZ proteins. Collectively, these results show that BIN2 interacts with JAZ proteins and plays a negative role in plant resistance to V. dahliae. Thus, BIN2 may be a potential target gene for genetic engineering against Verticillium wilt in crops.

SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.

Transcriptome-Wide Identification and Characterization of the JAZ Gene Family in Mentha canadensis L

Jasmonate ZIM-domain (JAZ) proteins are the crucial transcriptional repressors in the jasmonic acid (JA) signaling process, and they play pervasive roles in plant development, defense, and plant specialized metabolism. Although numerous JAZ gene families have been discovered across several plants, our knowledge about the JAZ gene family remains limited in the economically and medicinally important Chinese herb Mentha canadensis L. Here, seven non-redundant JAZ genes named McJAZ1–McJAZ7 were identified from our reported M. canadensis transcriptome data. Structural, amino acid composition, and phylogenetic analysis showed that seven McJAZ proteins contained the typical zinc-finger inflorescence meristem (ZIM) domain and JA-associated (Jas) domain as conserved as those in other plants, and they were clustered into four groups (A-D) and distributed into five subgroups (A1, A2, B1, B2, and D). Quantitative real-time PCR (qRT-PCR) analysis showed that seven McJAZ genes displayed differential expression patterns in M. canadensis tissues, and preferentially expressed in flowers. Furthermore, the McJAZ genes expression was differentially induced after Methyl jasmonate (MeJA) treatment, and their transcripts were variable and up- or down-regulated under abscisic acid (ABA), drought, and salt treatments. Subcellular localization analysis revealed that McJAZ proteins are localized in the nucleus or cytoplasm. Yeast two-hybrid (Y2H) assays demonstrated that McJAZ1-5 interacted with McCOI1a, a homolog of Arabidopsis JA receptor AtCOI1, in a coronatine-dependent manner, and most of McJAZ proteins could also form homo- or heterodimers. This present study provides valuable basis for functional analysis and exploitation of the potential candidate McJAZ genes for developing efficient strategies for genetic improvement of M. canadensis.

Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance

Plants are constantly threatened by pathogens, so have evolved complex defence signalling networks to overcome pathogen attacks. Post-translational modifications (PTMs) are fundamental to plant immunity, allowing rapid and dynamic responses at the appropriate time. PTM regulation is essential; pathogen effectors often disrupt PTMs in an attempt to evade immune responses. Here, we cover the mechanisms of disease resistance to pathogens, and how growth is balanced with defence, with a focus on the essential roles of PTMs. Alteration of defence-related PTMs has the potential to fine-tune molecular interactions to produce disease-resistant crops, without trade-offs in growth and fitness.

Interaction of BTB-TAZ protein MdBT2 and DELLA protein MdRGL3a regulates nitrate-mediated plant growth

Nitrate acts as a vital signal molecule in the modulation of plant growth and development. The phytohormones gibberellin (GA) is also involved in this process. However, the exact molecular mechanism of how nitrate and GA signaling pathway work together in regulating plant growth remains poorly understood. In this study, we found that a nitrate-responsive BTB/TAZ protein MdBT2 participates in regulating nitrate-induced plant growth in apple (Malus × domestica). Yeast two-hybridization, protein pull-down, and bimolecular fluorescence complementation (BiFC) assays showed that MdBT2 interacts with a DELLA protein MdRGL3a, which is required for the ubiquitination and degradation of MdRGL3a proteins via a 26S proteasome-dependent pathway. Furthermore, heterologous expression of MdBT2 partially rescued growth inhibition caused by overexpression of MdRGL3a in Arabidopsis. Taken together, our findings indicate that MdBT2 promotes nitrate-induced plant growth partially through reducing the abundance of the DELLA protein MdRGL3a.

Research progress of fruit color development in apple (Malus domestica Borkh.)

Apple (Malus domestica Borkh.) is one of the most widely produced and economically important fruits in temperate regions. Fruit color development in apple is a major focus for both breeders and researchers as consumers associate brightly colored red apples with ripeness and a good flavor. In recent years, great progress has been made in the research of apple fruit color development, but its development mechanism has not been systematic dissected from the aspects of genetics, transcription or environmental factors. Here, we summarize research on the coloration of apple fruit, including the development of important genomic databases to identify important genomic regions and genes, genetic and transcriptional factors that regulate pigment accumulation, environmental factors that affect anthocyanin synthesis, and the current breeding progress of red-skinned and red-fleshed apples. We describe key transcription factors, such as MYB, bHLH, and WD40, which are involved in the regulation of anthocyanin synthesis and fruit color development in apple. We also discuss the regulation of apple color by external environmental factors such as light, temperature, and water. The aim of this review is to provide insights into the molecular mechanisms underlying anthocyanin biosynthesis in apple. This information will provide significant guidance for the breeding of high-quality red-skinned and red-fleshed apple varieties.

Metabolite analysis reveals distinct spatio-temporal accumulation of anthocyanins in two teinturier variants of cv. 'Gamay' grapevines (Vitis vinifera L.)

White-fleshed grape cv. 'Gamay' and its two teinturier variants presented distinct spatial-temporal accumulation of anthocyanins, with uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. In most red grape cultivars, anthocyanins accumulate exclusively in the berry skin, while 'teinturier' cultivars also accumulate anthocyanins in the pulp. Here, we investigated the teinturier cvs. 'Gamay de Bouze' and 'Gamay Fréaux' (two somatic variants of the white-fleshed cv. 'Gamay') through metabolic and transcript analysis to clarify whether these two somatic variants have the same anthocyanin accumulation pattern in the skin and pulp, and whether primary metabolites are also affected. The skin of the three cultivars and the pulp of 'Gamay de Bouze' begun to accumulate anthocyanins at the onset of berry ripening. However, the pulp of 'Gamay Fréaux' exhibited a distinct anthocyanin accumulation pattern, starting as early as fruit set with very low level of sugars. The highest level of anthocyanins was found in 'Gamay Fréaux' skin, followed by 'Gamay de Bouze' and 'Gamay'. Consistently, the transcript abundance of genes involved in anthocyanin biosynthesis were in line with the anthocyanin levels in the three cultivars. Despite no evident differences in pulp sugar content, the concentration of glucose and fructose in the skin of 'Gamay Fréaux' was only half of those in the skin of 'Gamay' and 'Gamay de Bouze' throughout all berry ripening, suggesting an uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. The study provides a comprehensive view of metabolic consequences in grape somatic variants and the three almost isogenic genotypes can serve as ideal reagents to further uncover the mechanisms underlying the linkage between sugar and anthocyanin accumulation.

VvWRKY22 transcription factor interacts with VvSnRK1.1/VvSnRK1.2 and regulates sugar accumulation in grape

WRKY transcription factors are one of the largest transcriptional regulator families, involved in various signaling networks in plants. However, only limited functional exploration of the sugar signaling of Vitis vinifera WRKY22 transcription factor (VvWRKY22) has been conducted. In this study, the roles played by VvWRKY22 in sugar accumulation in grapes were investigated. VvWRKY22 was co-expressed with 16 sugar-related genes, and the expression of VvWRKY22 in grape suspension cells was inhibited by sucrose, and induced by fructose and abscisic acid (ABA). Results showed that over-expression of VvWRKY22 decreased the sucrose, glucose and fructose content, and regulated the expression levels of sugar and ABA-related genes. Moreover, it was found that VvWRKY22 interacted with VvSnRK1.1 or VvSnRK1.2 proteins (Sucrose non-fermenting-1-related protein kinase 1), which are important kinases related to sugar metabolism. These results, thus, provide new genetic evidences to support the view that VvWRKY22 functions in regulating sugar metabolism in grapes.

Genome-wide characterization and analysis of bHLH transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii)

As one of the largest transcription factor family, basic helix-loop-helix (bHLH) transcription factor family plays an important role in plant metabolism, physiology and growth. Berry color is one of the important factors that determine grape quality. However, the bHLH transcription factor family's function in anthocyanin synthesis of grape berry has not been studied systematically. We identified 115 bHLH transcription factors in grape genome and phylogenetic analysis indicated that bHLH family could be classified into 25 subfamilies. First, we screened six candidate genes by bioinformatics analysis and expression analysis. We found one of the candidate genes VdbHLH037 belonged to III (f) subfamily and interacted with genes related to anthocyanin synthesis through phylogenetic analysis and interaction network prediction. Therefore, we speculated that VdbHLH037 participated in the anthocyanin synthesis process. To confirm this, we transiently expressed VdbHLH037 in grape and Arabidopsis transformation. Compared with the control, transgenic materials can accumulate more anthocyanins. These results provide a good base to study the function of the VdbHLH family in anthocyanin synthesis of grape berry.

Peach PpSnRK1α interacts with bZIP11 and maintains trehalose balance in plants

The nonreducing disaccharide trehalose is widespread in nature. It plays a very important role in plant growth and development. In plants, trehalose is present in trace amounts. High concentration of trehalose disrupts energy balance and inhibits normal growth and development. Studies have shown that high levels of trehalose and trehalose-6-phosphate (T6P), the metabolic precursor of trehalose, inhibit sucrose non-fermenting-1-related protein kinase1 (SnRK1) activity, which affect plant growth and development. However, the role of SnRK1, the energy balance center, in the regulation of trehalose metabolism in plants is unknown. In this study, exogenous trehalose at higher concentrations inhibited the expression of SnRK1 genes, especially PpSnRK1α in peach (Prunus persica) seedlings. This change in gene expression was dependent on trehalose concentration. Furthermore, overexpression of peach PpSnRK1α in Arabidopsis thaliana significantly promoted trehalase activity, reduced T6P content, and suppressed the trehalose synthesis related genes (TPSs, TPPB) expression, promoted the trehalose metabolism of gene expression (TRE1), in addition the transgenic plants alleviated photosynthetic product distribution imbalance (aboveground and underground parts), and enhanced root growth. Yeast two-hybrid and bimolecular fluorescence assays revealed the interaction between PpSnRK1α and peach basic domain leucine zipper transcription factor 11 (PpbZIP11), a key transcription factor of trehalose metabolism, in the nucleus. To summarize, PpSnRK1α overexpression improved bZIP11 transcriptional activity and regulated trehalose metabolism to protect the plants against trehalose-induced damage. This study preliminarily explained the mechanism of SnRK1 regulating trehalose metabolism balance in plants, which laid a foundation for further understanding of energy metabolism and function of SnRK1 in plants.

Transcriptome analysis and association mapping reveal the genetic regulatory network response to cadmium stress in Populus tomentosa

Long non-coding RNAs (lncRNAs) play essential roles in plant abiotic stress responses, but the response of lncRNA-mediated genetic networks to cadmium (Cd) treatment remain elusive in trees, the promising candidates for phytoremediation of Cd contamination. We identified 172 Cd-responsive lncRNAs and 295 differentially expressed target genes in the leaves of Cd-treated Populus tomentosa. Functional annotation revealed that these lncRNAs were involved in various processes, including photosynthesis, hormone regulation, and phenylalanine metabolism. Association studies identified 78 significant associations, representing 14 Cd-responsive lncRNAs and 28 target genes for photosynthetic and leaf physiological traits. Epistasis uncovered 83 pairwise interactions among these traits, revealing Cd-responsive lncRNA-mediated genetic networks for photosynthesis and leaf physiology in P. tomentosa. We focused on the roles of two Cd-responsive lncRNA-gene pairs, MSTRG.22608.1-PtoMYB73 and MSTRG.5634.1-PtoMYB27, in Cd tolerance of Populus, and detected insertions/deletions within lncRNAs as polymorphisms driving target gene expression. Genotype analysis of lncRNAs and heterologous overexpression of PtoMYB73 and PtoMYB27 in Arabidopsis indicated their effects on enhancing Cd tolerance, photosynthetic rate, and leaf growth, and the potential interaction mechanisms of PtoMYB73 with abiotic stresses. Our study identifies the genetic basis for the response of Populus to Cd treatment, facilitating genetic improvement of Cd tolerance in trees.

Apple BT2 protein negatively regulates jasmonic acid-triggered leaf senescence by modulating the stability of MYC2 and JAZ2

Jasmonic acid (JA) is shown to induce leaf senescence. However, the underlying molecular mechanism is not well understood, especially in woody plants such as fruit trees. In this study, we are interested in exploring the biological role of MdBT2 in JA-mediated leaf senescence. We found that MdBT2 played an antagonistic role in MdMYC2-promoted leaf senescence. Our results revealed that MdBT2 interacted with MdMYC2 and accelerated its ubiquitination degradation, thus negatively regulated MdMYC2-promoted leaf senescence. In addition, MdBT2 acted as a stabilizing factor to improve the stability of MdJAZ2 through direct interaction, thereby inhibited JA-mediated leaf senescence. Furthermore, our results also showed that MdBT2 interacted with a subset of JAZ proteins in apple, including MdJAZ1, MdJAZ3, MdJAZ4 and MdJAZ8. Our investigations provide new insight into molecular mechanisms of JA-modulated leaf senescence. The dynamic JA-MdBT2-MdJAZ2-MdMYC2 regulatory module plays an important role in JA-modulated leaf senescence.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

Transcription Factors Rc and OsVP1 Coordinately Regulate Preharvest Sprouting Tolerance in Red Pericarp Rice

Red pericarp associates with seed dormancy or preharvest sprouting (PHS) tolerance in crops. To identify this association's molecular mechanism, a PHS mutant Osviviparous1 (Osvp1) was characterized in rice and crossed with Kasalath, a red pericarp cultivar with Rc (red coleoptiles) genotype. Among the dehulled seeds of F₂ progenies, RcRcvp1vp1 seeds performed a lower PHS rate than rcrcvp1vp1 seeds and showed shallower pigmentation than RcRcVP1VP1 seeds. Kasalath and SL9 (an RcRcVP1VP1 substitution line with Nipponbare background) showed more ABA sensitivity than the Nipponbare (rcrcVP1VP1) by the germination assay, and the transcriptional abundance of ABA signal genes OsABI2, OsSnRK2, OsVP1, ABI5, and especially OsVP1 increased in the red pericarp line SL9. Moreover, OsVP1 can directly bind Rc (bHLH) promoter by yeast one-hybrid, which activates Rc and OsLAR expression in red pericarp rice. Furthermore, a luciferase complementation imaging assay showed that OsVP1 interacts with transcriptions factors Rc and OsC1. These results indicate that OsVP1 promotes proanthocyanidin accumulation through the interaction among OsVP1, Rc, and OsC1 and then increases the plant's ABA sensitivity and PHS resistance.

Advances in Biosynthesis and Biological Functions of Proanthocyanidins in Horticultural Plants

Proanthocyanidins are colorless flavonoid polymers condensed from flavan-3-ol units. They are essential secondary plant metabolites that contribute to the nutritional value and sensory quality of many fruits and the related processed products. Mounting evidence has shown that the accumulation of proanthocyanidins is associated with the resistance of plants against a broad spectrum of abiotic and biotic stress conditions. The biosynthesis of proanthocyanidins has been examined extensively, allowing for identifying and characterizing the key regulators controlling the biosynthetic pathway in many plants. New findings revealed that these specific regulators were involved in the proanthocyanidins biosynthetic network in response to various environmental conditions. This paper reviews the current knowledge regarding the control of key regulators in the underlying proanthocyanidins biosynthetic and molecular mechanisms in response to environmental stress. Furthermore, it discusses the directions for future research on the metabolic engineering of proanthocyanidins production to improve food and fruit crop quality.