Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

ME2 Promotes Hepatocellular Carcinoma Cell Migration through Pyruvate

Cancer metastasis is still a major challenge in clinical cancer treatment. The migration and invasion of cancer cells into surrounding tissues and blood vessels is the primary step in cancer metastasis. However, the underlying mechanism of regulating cell migration and invasion are not fully understood. Here, we show the role of malic enzyme 2 (ME2) in promoting human liver cancer cell lines SK-Hep1 and Huh7 cells migration and invasion. Depletion of ME2 reduces cell migration and invasion, whereas overexpression of ME2 increases cell migration and invasion. Mechanistically, ME2 promotes the production of pyruvate, which directly binds to β-catenin and increases β-catenin protein levels. Notably, pyruvate treatment restores cell migration and invasion of ME2-depleted cells. Our findings provide a mechanistic understanding of the link between ME2 and cell migration and invasion.

Comparative analysis of two kinds of garlic seedings: qualities and transcriptional landscape

BACKGROUND

Facility cultivation is widely applied to meet the increasing demand for high yield and quality, with light intensity and light quality being major limiting factors. However, how changes in the light environment affect development and quality are unclear in garlic. When garlic seedlings are grown, they can also be exposed to blanching culture conditions of darkness or low-light intensity to ameliorate their appearance and modify their bioactive compounds and flavor.

RESULTS

In this study, we determined the quality and transcriptomes of 14-day-old garlic and blanched garlic seedlings (green seedlings and blanched seedlings) to explore the mechanisms by which seedlings integrate light signals. The findings revealed that blanched garlic seedlings were taller and heavier in fresh weight compared to green garlic seedlings. In addition, the contents of allicin, cellulose, and soluble sugars were higher in the green seedlings. We also identified 3,872 differentially expressed genes between green and blanched garlic seedlings. The Kyoto Encyclopedia of Genes and Genomes analysis suggested enrichment for plant-pathogen interactions, phytohormone signaling, mitogen-activated protein kinase signaling, and other metabolic processes. In functional annotations, pathways related to the growth and formation of the main compounds included phytohormone signaling, cell wall metabolism, allicin biosynthesis, secondary metabolism and MAPK signaling. Accordingly, we identified multiple types of transcription factor genes involved in plant-pathogen interactions, plant phytohormone signaling, and biosynthesis of secondary metabolites among the differentially expressed genes between green and blanched garlic seedlings.

CONCLUSIONS

Blanching culture is one facility cultivation mode that promotes chlorophyll degradation, thus changing the outward appearance of crops, and improves their flavor. The large number of DEGs identified confirmed the difference of the regulatory machinery under two culture system. This study increases our understanding of the regulatory network integrating light and darkness signals in garlic seedlings and provides a useful resource for the genetic manipulation and cultivation of blanched garlic seedlings.

Comparative genomics analysis of drought response between obligate CAM and C3 photosynthesis plants

Crassulacean acid metabolism (CAM) plants exhibit elevated drought and heat tolerance compared to C₃ and C₄ plants through an inverted pattern of day/night stomatal closure and opening for CO₂ assimilation. However, the molecular responses to water-deficit conditions remain unclear in obligate CAM species. In this study, we presented genome-wide transcription sequencing analysis using leaf samples of an obligate CAM species Kalanchoë fedtschenkoi under moderate and severe drought treatments at two-time points of dawn (2-h before the start of light period) and dusk (2-h before the dark period). Differentially expressed genes were identified in response to environmental drought stress and a whole genome wide co-expression network was created as well. We found that the expression of CAM-related genes was not regulated by drought stimuli in K. fedtschenkoi. Our comparative analysis revealed that CAM species (K. fedtschenkoi) and C₃ species (Arabidopsis thaliana, Populus deltoides 'WV94') share some common transcriptional changes in genes involved in multiple biological processes in response to drought stress, including ABA signaling and biosynthesis of secondary metabolites.

Impacts of Intercropped Maize Ecological Shading on Tea Foliar and Functional Components, Insect Pest Diversity and Soil Microbes

Ecological shading fueled by maize intercropping in tea plantations can improve tea quality and flavor, and efficiently control the population occurrence of main insect pests. In this study, tea plants were intercropped with maize in two planting directions from east to west (i.e., south shading (SS)) and from north to south (i.e., east shading (ES) and west shading (WS)) to form ecological shading, and the effects on tea quality, and the population occurrence and community diversity of insect pests and soil microbes were studied. When compared with the non-shading control, the tea foliar nutrition contents of free fatty acids have been significantly affected by the ecological shading. SS, ES, and WS all significantly increased the foliar content of theanine and caffeine and the catechin quality index in the leaves of tea plants, simultaneously significantly reducing the foliar content of total polyphenols and the phenol/ammonia ratio. Moreover, ES and WS both significantly reduced the population occurrences of Empoasca onukii and Trialeurodes vaporariorum. Ecological shading significantly affected the composition of soil microbial communities in tea plantations, in which WS significantly reduced the diversity of soil microorganisms.

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L

The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in Arabidopsis thaliana L. using resources GEO NCBI, string-db, ShinyGO, STREME, and Tomtom, as well as programs metaRE, CisCross, and Cytoscape. Through the meta-analysis of five transcriptomic experiments, we selected a set of 1151 differentially expressed genes, including 453 genes that compose the gene network. Ten significantly enriched regulatory motifs for TFs families ZF-HD, HB, C2H2, NAC, BZR, and ARID were found in the promoter regions of differentially expressed genes. In addition, we predicted families of transcription factors associated with the duration of exposure (RAV, HSF), intensity of high light treatment (MYB, REM), and the direction of gene expression change (HSF, S1Fa-like). We predicted genetic components systems involved in a high light response and their expression changes, potential transcriptional regulators, and associated processes.

Identification and Characterization of SOG1 (Suppressor of Gamma-Response 1) Homologues in Plants Using Data Mining Resources and Gene Expression Profiling

SOG1 (Suppressor of the Gamma response 1) is the master-regulator of plant DNA damage response (DDR), a highly coordinated network of DNA damage sensors, transducers, mediators, and effectors, with highly coordinated activities. SOG1 transcription factor belongs to the NAC/NAM protein family, containing the well-conserved NAC domain and five serine-glutamine (SQ) motifs, preferential targets for phosphorylation by ATM and ATR. So far, the information gathered for the SOG1 function comes from studies on the model plant Arabidopsis thaliana. To expand the knowledge on plant-specific DDR, it is opportune to gather information on other SOG1 orthologues. The current study identified plants where multiple SOG1 homologues are present and evaluated their functions by leveraging the information contained in publicly available transcriptomics databases. This analysis revealed the presence of multiple SOG1 sequences in thirteen plant species, and four (Medicago truncatula, Glycine max, Kalankoe fedtschenkoi, Populus trichocarpa) were selected for gene expression data mining based on database availability. Additionally, M. truncatula seeds and seedlings exposed to treatments known to activate DDR pathways were used to evaluate the expression profiles of MtSOG1a and MtSOG1b. The experimental workflow confirmed the data retrieved from transcriptomics datasets, suggesting that the SOG1 homologues have redundant functions in different plant species.

PpSnRK1α overexpression alters the response to light and affects photosynthesis and carbon metabolism in tomato

Sucrose nonfermentation 1 (SNF1) related kinase 1 (SnRK1) is a central energy sensor kinase in plants and a key switch regulating carbon and nitrogen metabolism. Fruit quality depends on leaf photosynthetic efficiency and carbohydrate accumulation, but the role of peach (Prunus persica) SnRK1 α subunit (PpSnRK1α) in regulating leaf carbon metabolism and the light signal response remains unclear. We studied the carbon metabolism of tomato leaves overexpressing PpSnRK1α and the responses of PpSnRK1α-overexpressing tomato leaves to light signals. Transcriptome, metabolome, and real-time quantitative polymerase chain reaction analyses revealed that uridine 5'-diphosphoglucose, glutamate, and glucose-6-phosphate accumulated in tomato leaves overexpressing PpSnRK1α. The expression of genes (e.g., GDH2, SuSy) encoding enzymes related to carbon metabolism (e.g., glutamate dehydrogenase (GDH2; EC: 1.4.1.3), sucrose synthase (SS; EC: 2.4.1.13)) and chlorophyllase (CLH) encoding chlorophyllase (EC: 3.1.1.14), which regulates photosynthetic pigments and photosynthesis, was significantly increased in PpSnRK1α-overexpressing plants. PpSnRK1α overexpression inhibited the growth of hypocotyls and primary roots in response to light. The chlorophyll content of the leaves was increased, the activity of SS and ADPG pyrophosphatase (AGPase; EC: 2.7.7.27) was increased, and photosynthesis was promoted in PpSnRK1α-overexpressing plants relative to wild-type plants. Under light stress, the net photosynthetic rate of plants was significantly higher in plants overexpressing PpSnRK1α than in wild-type plants. This indicates that PpSnRK1α promotes the accumulation of carbohydrates by regulating genes related to carbon metabolism, regulating genes related to chlorophyll synthesis, and then responding to light signals to increase the net photosynthetic rate of leaves.

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

BACKGROUND

Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied.

RESULTS

Here we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12 h/12 h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 440, and 1,000 μmol m-2 s-1) based on RNA sequencing performed for mature leaf samples collected at dawn (2 h before the light period) and dusk (2 h before the dark period). An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Measurements of leaf titratable acidity, soluble sugar, and starch turnover provided metabolic indicators of the magnitude of CAM under the different light treatments and were used to provide biological context for the expression dataset. Furthermore, CAM-related subnetworks were highlighted to showcase genes relevant to CAM pathway, circadian clock, and stomatal movement. In comparison with white light, monochrome blue/red/far-red light treatments repressed the expression of several CAM-related genes at dusk, along with a major reduction in acid accumulation. Increasing light intensity from an intermediate level (440 μmol m-2 s-1) of white light to a high light treatment (1,000 μmol m-2 s-1) increased expression of several genes involved in dark CO2 fixation and malate transport at dawn, along with an increase in organic acid accumulation.

CONCLUSIONS

This study provides a useful genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants. Our results support the hypothesis that both light intensity and light quality can modulate the CAM pathway through regulation of CAM-related genes in K. fedtschenkoi.