Exogenous substances can enhance plant tolerance to low-temperature stress through five primary mechanisms. The rational application of these substances during early spring cold snaps and other unexpected low-temperature events at various growth stages can effectively mitigate crop damage and ensure stable yields. Low-temperature stress (LTS) is one of the main abiotic stress factors limiting plant growth and development and crop yield. It severely affects plant yield and even causes death by interfering with cell membrane stability, inhibiting photosynthesis, and causing metabolic imbalance. In recent years, exogenous substances (ESs) regulation technology has become an important research direction for improving plants’ resistance to LTS due to its high efficiency and operability. Multiple ESs have been shown to effectively alleviate LTS in plants. This paper systematically reviews the research findings on 82 ESs from 121 literature sources and summarizes the molecular physiological mechanisms by which these substances alleviate LTS. The mechanisms of action mainly include the following five aspects: (1) enhancing the antioxidant defense system; (2) optimizing plant hormone balance; (3) maintaining and enhancing photosynthetic efficiency; (4) accumulating osmoprotective substances; (5) improving plant nutritional status. In addition, we explored in depth how to effectively utilize exogenous substances with potential and efficiency to address the challenges posed by LTS in agricultural production. This paper summarizes the research progress on the mechanisms of exogenous substances in resisting LTS, providing theoretical basis and technical support for crop cultivation and stable production in response to LTS.

Cyclic lipopeptides secreted by the probiotic bacterium Bacillus subtilis have attracted much attention due to their antitumor activities and low toxicity. However, the role of Mycosubtilin (Myco) in the prevention and treatment of cervical cancer remains unclear. In the present study, we conducted a systematic evaluation of Myco’s anti-cervical cancer effects to identify its molecular mechanism of action using proteomics technology. The results reveal that Myco inhibited the growth of HeLa and SiHa cervical cancer cell lines in a dose-dependent (3–15 µg/mL) and time-dependent (12–48 h) manner and significantly reduced colony formation and migration in HeLa cells, highlighting its potential to suppress tumor spread. Moreover, autophagosome and autolysosome numbers were significantly increased after Myco treatment, and the expression of autophagy-related proteins was significantly modulated, suggesting that autophagy plays a role in its anti-cancer mechanism. Myco treatment also induced G1 phase cell cycle arrest in HeLa cells, as confirmed by proteomics analysis. Myco was shown to induce cell cycle arrest in HeLa cells by regulating the P53 pathway and autophagy-dependent cell death via the PI3K/AKT/mTOR signaling pathway, demonstrating its multidimensional effect on cervical cancer cell growths. Myco treatment significantly inhibited tumor growth in vivo in a nude mouse cervical cancer xenograft model, providing direct evidence of its potential as a therapeutic candidate for cervical cancer. Given its unique anti-cancer mechanism and significant therapeutic efficacy, Myco should be considered a promising therapeutic agent for cervical cancer.

Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca2+]i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments.

Our previous study reported that the metabolite of Bacillus subtilis BS-Z15 n-butanol site could reduce body weight gain in mice, showing anti-obesity effects. This study further demonstrated the effects of purified mycosubtilin on the body weight gain and gut microbiota of Kunming mice. 30 male Kunming white mice were randomly selected into three groups at four weeks of age: Control (group A), gavage-administered with saline daily; n-butanol site treated (group B), gavage-administered with n-butanol site metabolites (90 mg/kg); and mycosubtilin treated (group C), gavage-administered with mycosubtilin (6 mg/kg). Different groups' gut microbiota compositions were analyzed using high-throughput sequencing technology. The results showed that the effects of mycosubtilin and n-butanol sites were consistent; the treatment groups showed a significant reduction in body weight gain as well as triglyceride and low-density lipoprotein contents as compared to the control group ( P < 0.05). Moreover, the size and contents of epididymal adipocytes were also significantly reduced ( P < 0.05), and the gavage administration of mycosubtilin could significantly increase the expression levels of lipolysis gene adipose triglyceride lipase ( ATGL ) in the mice liver. Mycosubtilin and n-butanol site treatments could significantly alter the composition of the gut microbiota as compared to the physiologic saline treatment. B. subtilis BS-Z15 metabolites may regulate weight gain primarily by mycosubtilin, according to these findings. The mycosubtilin might reduce weight gain in mice by regulating lipid metabolism, thereby reducing fat accumulation and altering the composition of gut microbiota.

棉花黄萎病是导致棉花减产的主要土传病害之一,在前期工作中筛选到1株对棉花黄萎病病原菌——大丽轮枝菌(Ver-ticillium dahliae)具有较强拮抗作用的枯草芽孢杆菌J-15菌株.为了揭示施用枯草芽孢杆菌J-15次生代谢产物(secondary me-tabolites of Bacillus subtilis J-15,SMs)对棉田土壤细菌群落多样性的影响规律.将含有大丽轮枝菌的盆栽分为2组,室温黑暗环境下进行培养,模拟该代谢产物施入土壤的情况,其中实验组为添加0.33 mg·mL-1SMs至土壤最大含水量,对照组为添加等量的去离子水.分别在0、10、30和60 d取样,采用Soil DNA Kit试剂盒提取土壤微生物的总DNA,利用高通量测序技术分析棉田土壤细菌群落结构.根据Alpha多样性分析可知,SMs处理土壤后的Shannon、Simpson、Chao1和Ace指数与对照组均无显著差异,说明SMs对土壤中细菌群落的丰富度和多样性无明显影响.根据群落结构分析可知,SMs处理土壤10、30和60 d后,变形菌门和硬壁菌门的相对丰度略微上升,但差异均不显著.属水平上,SMs处理土壤10 d和30 d后,假单胞菌属和芽孢杆菌属的相对丰度略有上升,但差异均不显著.这说明在土壤中施用SMs虽在一定程度上改变了土壤中细菌群落结构但影响却并不显著.由此推断SMs对棉田土壤细菌群落结构及多样性无显著影响,为开发利用枯草芽孢杆菌J-15进行农业上的生物防治提供了依据.

The lipopeptides produced by Bacillus subtilis have anti-cancer potential. We had previously identified a secondary metabolite of B. subtilis strain Z15 (BS-Z15), which has an operon that regulates lipopeptide synthesis, and also demonstrated that the fermentation products of this strain exerted antioxidant and pro-immune effects. The purpose of this study was to investigate in vitro and in vivo the anticancer effects of BS-Z15 secondary metabolites (BS-Z15 SMs) on hepatocellular carcinoma (HCC) cells. BS-Z15 SMs significantly inhibited H22 cell-derived murine xenograft tumor growth without any systemic toxicity. In addition, BS-Z15 SMs decreased the viability of H22 cells and BEL-7404 cells in vitro with respective IC50 values of 33.83 and 27.26 mu g/mL. Consistent with this, BS-Z15 SMs induced apoptosis and G0/G1 phase arrest in the BEL-7404 cells, and the mitochondrial membrane potential was also significantly reduced in a dose-dependent manner. Mechanistically, BS-Z15 SMs upregulated the pro-apoptotic p53, Bax, cytochrome C, and cleaved-caspase-3/9 proteins and downregulated the anti-apoptotic Bcl-2. These findings suggest that the induction of apoptosis in HCC cells by BS-Z15 SMs may be related to the mitochondrial pathway. Thus, the secondary metabolites of B. subtilis strain Z15 are promising to become new anti-cancer drugs for the clinical treatment of liver cancer.

Microbial-plant interactions protect plants from external stimuli, releasing various elicitor that activate the plants defense response and regulate its growth. Bacillus subtilis BS-Z15 was screened from cotton inter-rhizosphere soil, antagonized various plant pathogens, and protected cotton against Verticillium dahliae. This study showed that the BS-Z15 lipopeptide mycosubtilin homologue could act as an elicitor to induce systemic resistance (ISR) in plants. Mycosubtilin homologue induced ROS burst and deposition, callose deposition, MAPK cascade phosphorylation, and up-regulated PR1 and PDF1.2 gene expression in Arabidopsis seedlings, moreover enhanced resistance of Arabidopsis to Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000) and V. dahliae. Transcriptome analysis was then used to evaluate the impact of mycosubtilin homologue on plant gene expression control. Mycosubtilin homologues activated Arabidopsis ISR on genes in metabolic pathways such as Arabidopsis plant-pathogen interactions, phenylpropanoid biosynthesis, MAPK signaling pathway, and phytohormone signaling. These analyses revealed that mycosubtilin homologues mediate the regulation of plant systemic resistance and growth and development by affecting related metabolites in glycolysis and gluconeogenesis, pentose phosphate pathway, tricarboxylic acid cycle, and amino acid metabolism in Arabidopsis. These findings confirmed that a mycosubtilin homologue could trigger the initiation of the Arabidopsis ISR by interacting with a variety of PTI components and transcriptional metabolic signaling pathways.

BackgroundPrevious studies have shown that secondary metabolites of Bacillus subtilis strain Z15 (BS-Z15) are effective in treating fungal infections in mice. To evaluate whether it also modulates immune function in mice to exert antifungal effects, we investigated the effect of BS-Z15 secondary metabolites on both the innate and adaptive immune functions of mice, and explored its molecular mechanism through blood transcriptome analysis.ResultsThe study showed that BS-Z15 secondary metabolites increased the number of monocytes and platelets in the blood, improved natural killer (NK) cell activity and phagocytosis of monocytes-macrophages, increased the conversion rate of lymphocytes in the spleen, the number of T lymphocytes and the antibody production capacity of mice, and increased the levels of Interferon gamma (IFN-gamma), Interleukin-6 (IL-6), Immunoglobulin G (IgG) and Immunoglobulin M (IgM) in plasma. The blood transcriptome analysis revealed 608 differentially expressed genes following treatment with BS-Z15 secondary metabolites, all of which were significantly enriched in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms for immune-related entries and pathways such as Tumor Necrosis Factor (TNF) and Toll-like receptor (TLR) signaling pathways, and upregulated expression levels of immune-related genes such as Complement 1q B chain (C1qb), Complement 4B (C4b), Tetracyclin Resistant (TCR) and Regulatory Factor X, 5 (RFX5).ConclusionsBS-Z15 secondary metabolites were shown to enhance innate and adaptive immune function in mice, laying a theoretical foundation for its development and application in the field of immunity.

Verticillium wilt is a kind of soil-borne plant fungal disease caused by Verticillium dahliae (Vd). Vd 991 is a strong pathogen causing cotton Verticillium wilt. Previously, we isolated a compound from the secondary metabolites of Bacillus subtilis J15 (BS J15), which showed a significant control effect on cotton Verticillium wilt and was identified as C17 mycosubtilin. However, the specific fungistatic mechanism by which C17 mycosubtilin antagonizes Vd 991 is not clear. Here, we first showed that C17 mycosubtilin inhibits the growth of Vd 991 and affects germination of spores at the minimum inhibitory concentration (MIC). Morphological observation showed that C17 mycosubtilin treatment caused shrinking, sinking, and even damage to spores; the hyphae became twisted and rough, the surface was sunken, and the contents were unevenly distributed, resulting in thinning and damage to the cell membrane and cell wall and swelling of mitochondria of fungi. Flow cytometry analysis with ANNEXINV-FITC/PI staining showed that C17 mycosubtilin induces necrosis of Vd 991 cells in a time-dependent manner. Differential transcription analysis showed that C17 mycosubtilin at a semi-inhibitory concentration (IC50) treated Vd 991 for 2 and 6 h and inhibited fungal growth mainly by destroying synthesis of the fungal cell membrane and cell wall, inhibiting its DNA replication and transcriptional translation process, blocking its cell cycle, destroying fungal energy and substance metabolism, and disrupting the redox process of fungi. These results directly showed the mechanism by which C17 mycosubtilin antagonizes Vd 991, providing clues for the mechanism of action of lipopeptides and useful information for development of more effective antimicrobials.

Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding genes (PCGs). Here, we conducted a comprehensive bioinformatics analysis to identify a total of 9414 long noncoding RNAs (lncRNAs) in the seed coats of purple and white hulless barley along a developmental gradient. Transcriptome-wide profiles of lncRNAs documented several properties, including GC content fluctuation, uneven length, a diverse range of exon numbers, and a wide variety of transcript classifications. We found that certain lncRNAs in hulless barley possess detectable sequence conservation with Hordeum vulgare and other monocots. Furthermore, both differentially expressed lncRNAs (DElncRNAs) and PCGs (DEPCGs) were concentrated in the later seed development stages. On the one hand, DElncRNAs could potentially cis-regulate DEPCGs associated with multiple metabolic pathways, including flavonoid and anthocyanin biosynthesis in the late milk and soft dough stages. On the other hand, there was an opportunity for trans-regulated lncRNAs in the color-forming module to affect seed coat color by upregulating PCGs in the anthocyanin pathway. In addition, the interweaving of hulless barley lncRNAs and diverse TFs may function in seed coat coloration. Notably, we depicted a dynamic portrait of the anthocyanin synthesis pathway containing hulless barley lncRNAs. Therefore, this work provides valuable gene resources and more insights into the molecular mechanisms underlying anthocyanin accumulation in hulless barley from the perspective of lncRNAs, which facilitate the development of molecular design breeding in crops.

Aspergillus flavus can cause mildew in corn, peanuts, and other foods as well as animal feed, which seriously endangers human and livestock health; thus, preventing A. flavus contamination is imperative. Previous studies have found that the secondary metabolites of Bacillus subtilis BS-Z15 have broad-spectrum-inhibiting fungal activity, further confirming that the main active inhibiting fungal substance is Mycosubtilin (Myco). In this paper, corn and peanuts were treated with 0, 100, and 200 μg/mL BS-Z15 secondary metabolites (BS-Z15-SMA) for 7 days, and the aflatoxin contamination prevention effect was examined. The results showed that with increasing BS-Z15-SMA concentration, the aflatoxin contamination prevention effect was significantly enhanced. The above toxicity phenomena became more significant with extended BS-Z15-SMA treatment time. Scanning electron microscopy showed that 4 μg/mL Myco treatment resulted in a dented A. flavus surface and breakage of both the conidial stem and the mycelium. Transcriptome results showed that Myco significantly affected gene expression in A. flavus spores. The downregulated genes were significantly enriched in cell wall synthesis, transcription and translation, transmembrane transport pathways, and pathways related to key enzymes for aflatoxin synthesis. These results suggest that Myco could be used as a new bioactive material to prevent aflatoxin synthesis and contamination.

Ethylene response factor (ERF) Group VII members generally function in regulating plant growth and development, abiotic stress responses, and plant immunity in Arabidopsis; however, the details of the regulatory mechanism by which Group VII ERFs mediate plant immune responses remain elusive. Here, we characterized one such member, ERF72, as a positive regulator that mediates resistance to the necrotrophic pathogen Botrytis cinerea. Compared with the wild-type (WT), the erf72 mutant showed lower camalexin concentration and was more susceptible to B. cinerea, while complementation of ERF72 in erf72 rescued the susceptibility phenotype. Moreover, overexpression of ERF72 in the WT promoted camalexin biosynthesis and increased resistance to B. cinerea. We identified the camalexin-biosynthesis genes PAD3 and CYP71A13 and the transcription factor WRKY33 as target genes of ERF72. We also determined that MPK3 and MPK6 phosphorylated ERF72 at Ser151 and improved its transactivation activity, resulting in increased camalexin concentration and increased resistance to B. cinerea. Thus, ERF72 acts in plant immunity to coordinate camalexin biosynthesis both directly by regulating the expression of biosynthetic genes and indirectly by targeting WRKK33.

In our previous study, we identified a metabolite of Bacillus subtilis BS-Z15 (a strain with probiotic characteristics) that could improve immunity in mice. In the present study, we examined the effects of B. subtilis BS-Z15 and its metabolites on body weight gain and the intestinal microbiota of mice. Sixty 25-day-old male Kunming white mice were selected and randomly divided into four groups: control group (A), daily saline gavage; B. subtilis-treated group (B), single gavage (1 × 109 CFU/time/animal/day); group D, 14 consecutive gavages (1 × 109 CFU/time/animal/day); and B. subtilis metabolite-treated group (E), 30 consecutive gavages (90 mg kg−1/time/animal/day). High-throughput sequencing technology was used to analyze intergroup differences in the mouse intestinal microbiota. The results showed that the three treated groups had significantly slower body weight gain compared with the control group, which lasted until the 45 days (P < 0.05), and the daily food intake of the treated mice was higher (P < 0.05). The intestinal microbiota structure of the mice in the treated groups was significantly altered compared with that in the control group, suggesting that B. subtilis BS-Z15 may regulate the weight gain of animals by affecting their intestinal bacterial composition. After stopping the gavage of B. subtilis BS-Z15, the abundance of this strain in the small intestine of the mice gradually decreased and its presence was undetectable at 45 days, indicating that B. subtilis BS-Z15 could not colonize the intestine of these mice. These findings suggest that B. subtilis BS-Z15 may regulate intestinal microbiota through its metabolites to reduce weight gain.

Long noncoding RNAs (lncRNAs) play important regulatory roles in caryopsis development and grain size in rice. However, whether there exist differences in lncRNA expression between caryopses located on primary branches (CPB) and caryopses located on secondary branches (CSB) that contribute to their differential development remains elusive. Here, we performed transcriptome-wide analysis to identify 2,273 lncRNAs expressed in CPB and CSB at 0, 5, 12, and 20 days after flowering (DAF). Although these lncRNAs were widely distributed, the majority were located in intergenic regions of the 12 rice chromosomes. Based on gene expression cluster analysis, lncRNAs expressed in CPB and CSB were clustered into two subtypes in a position-independent manner: one includes 0- and 5-DAF CPB and CSB, and 12-DAF CSB; the second includes 12-DAF CPB and 20-DAF CPB and CSB. Furthermore, according to the expression value of each lncRNA, K-means cluster analysis revealed 135 early-stage, 116 middle-stage, and 114 late-stage expression-delayed lncRNAs in CSB. Then, we analyzed the expression values of the expression-delayed lncRNAs and nearby coding genes (100 kb upstream and downstream of the lncRNAs), and found 631 lncRNA-mRNA pairs, including 258 lncRNAs and 571 nearby coding genes, some of which are related to hormone-regulated grain development. These results suggested that expression-delayed lncRNAs in CSB may regulate the development of CPB and CSB, providing insight into the mechanism underlying the developmental differences between CPB and CSB, and the differences in grain yield.

Subtilisin-like proteases (SUBs), which are extensively distributed in three life domains, affect all aspects of the plant life cycle, from embryogenesis and organogenesis to senescence. To explore the role of SUBs in rice caryopsis development, we recharacterized the OsSUB gene family in rice (Oryza sativa ssp. japonica). In addition, investigation of the SUBs was conducted across cultivated and wild rice in seven other Oryza diploid species (O. brachyantha, O. glaberrima, O. meridionalis, O. nivara, O. punctata, O. rufipogon, and O. sativa ssp. indica). Sixty-two OsSUBs were identified in the latest O. sativa ssp. japonica genome, which was higher than that observed in wild species. The SUB gene family was classified into six evolutionary branches, and SUB1 and SUB3 possessed all tandem duplication (TD) genes. All paralogous SUBs in eight Oryza plants underwent significant purifying selection. The expansion of SUBs in cultivated rice was primarily associated with the occurrence of tandem duplication events and purifying selection and may be the result of rice domestication. Combining the expression patterns of OsSUBs in different rice tissues and qRT–PCR verification, four OsSUBs were expressed in rice caryopses. Moreover, OsSUBs expressed in rice caryopses possessed an earlier origin in Oryza, and the gene cluster formed by OsSUBs together with the surrounding gene blocks may be responsible for the specific expression of OsSUBs in caryopses. All the above insights were inseparable from the continuous evolution and domestication of Oryza. Together, our findings not only contribute to the understanding of the evolution of SUBs in cultivated and wild rice but also lay the molecular foundation of caryopsis development and engineering improvement of crop yield.

Bacillus subtilis J-15 is a plant growth-promoting rhizobacteria isolated from the soil rhizosphere of cotton and is resistant to cotton verticillium wilt. This study evaluated the effects of metabolites of J-15 (J-15-Ms), including mycosubtilin, on plant growth using Arabidopsis and cotton plants. The results showed that J-15-Ms promoted Arabidopsis seeding growth at lower concentrations of 0.2 μg/mL but inhibited the growth at higher concentrations, such as 20 μg/mL. Similar results were obtained in cotton. Thus, J-15-Ms-treated plants showed low-concentration-induced growth promotion and high-concentration-induced growth inhibition. The J-15-Ms components were analyzed by liquid chromatography–mass spectrometry. Correlation analysis using the J-15 genomic databases suggested that J-15 may synthesize indoleacetic acid via the indole-3-pymvate pathway and indole-3-acetamide pathway. Treatment with mycosubtilin, a purified peptide from J-15-Ms, showed that the peptide promoted Arabidopsis growth at a low concentration (0.1 μg/mL) and inhibited plant growth at high concentrations (higher than 1 μg/mL), which also significantly increased plant lateral root number. Transcriptomic analysis showed that mycosubtilin might promote lateral root development and inhibit plant primary root growth by regulating the expression of the plant hormone signaling pathway. This study reveals the mechanism of Bacillus subtilis J-15 in affecting plant growth.

OSCA (reduced hyperosmolality-induced [Ca2+]i increase) is a family of mechanosensitive calcium-permeable channels that play a role in osmosensing and stomatal immunity in plants. Oryza sativa has 11 OsOSCA genes; some of these were shown to complement hyperosmolality-induced [Ca2+]cyt increases (OICIcyt), salt stress-induced [Ca2+]cyt increases (SICIcyt), and the associated growth phenotype in the Arabidopsis thaliana mutant osca1. However, their biological functions in rice remain unclear. In this paper, we found that OsOSCA1.1 mediates OICIcyt and SICIcyt in rice roots, which are critical for stomatal closure, plant survival, and gene expression in shoots, in response to hyperosmolality and the salt stress treatment of roots. Compared with wild-type (Zhonghua11, ZH11) plants, OICIcyt and SICIcyt were abolished in the roots of 10-day-old ososca1.1 seedlings, in response to treatment with 250 mM of sorbitol and 100 mM of NaCl, respectively. Moreover, hyperosmolality- and salt stress-induced stomatal closure were also disrupted in a 30-day-old ososca1.1 mutant, resulting in lower stomatal resistance and survival rates than that in ZH11. However, overexpression of OsOSCA1.1 in ososca1.1 complemented stomatal movement and survival, in response to hyperosmolality and salt stress. The transcriptomic analysis further revealed the following three types of OsOSCA1.1-regulated genes in the shoots: 2416 sorbitol-responsive, 2349 NaCl-responsive and 1844 common osmotic stress-responsive genes after treated with 250 mM of sorbitol and 125 mM NaCl of in 30-day-old rice roots for 24 h. The Gene Ontology enrichment analysis showed that these OsOSCA1.1-regulated genes were relatively enriched in transcription regulation, hormone response, and phosphorylation terms of the biological processes category, which is consistent with the Cis-regulatory elements ABRE, ARE, MYB and MYC binding motifs that were overrepresented in 2000-bp promoter regions of these OsOSCA1.1-regulated genes. These results indicate that OsOSCA-mediated calcium signaling specifically regulates gene expression, in response to drought and salt stress in rice.

Calcium acts as a universal secondary messenger that transfers developmental cues and stress signals for gene expression and adaptive growth. A prior study showed that abiotic stresses induce mutually independent cytosolic Ca2+ ([Ca2+](cyt)) and nucleosolic Ca2+ ([Ca2+](nuc)) increases in Arabidopsis thaliana root cells. However, gene expression networks deciphering [Ca2+](cyt) and [Ca2+](nuc) signalling pathways remain elusive. Here, using transgenic A. thaliana to selectively impair abscisic acid (ABA)- or methyl jasmonate (MeJA)-induced [Ca2+](cyt) and [Ca2+](nuc) increases, we identified [Ca2+](cyt)- and [Ca2+](nuc)-regulated ABA- or MeJA-responsive genes with a genome oligo-array. Gene co-expression network analysis revealed four Ca2+ signal-decoding genes, CAM1, CIPK8, GAD1, and CPN20, as hub genes co-expressed with Ca2+-regulated hormone-responsive genes and hormone signalling genes. Luciferase complementation imaging assays showed interactions among CAM1, CIPK8, and GAD1; they also showed interactions with several proteins encoded by Ca2+-regulated hormone-responsive genes. Furthermore, CAM1 and CIPK8 were required for MeJA-induced stomatal closure; they were associated with ABA-inhibited seed germination. Quantitative reverse transcription polymerase chain reaction analysis showed the unique expression pattern of [Ca2+]-regulated hormone-responsive genes in cam1, cipk8, and gad1. This comprehensive understanding of distinct Ca2+ and hormonal signalling will allow the application of approaches to uncover novel molecular foundations for responses to developmental and stress signals in plants.

Long noncoding RNAs (lncRNAs) are distributed in various species and play critical roles in plant growth, development, and defence against stimuli. However, the lncRNA response to methyl jasmonate (MeJA) treatment has not been well characterized in Nicotiana tabacum Bright Yellow-2 (BY-2) cells, and their roles in plant defence remain elusive. Here, 7848 reliably expressed lncRNAs were identified in BY-2 cells, of which 629 differentially expressed (DE) lncRNAs were characterized as MeJA-responsive lncRNAs. The lncRNAs in BY-2 cells had a strong genus specificity in Nicotiana. The combined analysis of the cis-regulated lncRNAs and their target genes revealed the potential up- and downregulated target genes that are responsible for different biological functions and metabolic patterns. In addition, some lncRNAs for response-associated target genes might be involved in plant defence and stress resistance via their MeJA- and defence-related cis-regulatory elements. Moreover, some MeJA-responsive lncRNA target genes were related to quinolinate phosphoribosyltransferase, lipoxygenases, and endopeptidase inhibitors, which may contribute to nicotine synthesis and disease and insect resistance, indicating that MeJA-responsive lncRNAs regulate nicotine biosynthesis and disease resistance by regulating their potential target genes in BY-2 cells. Therefore, our results provide more targets for genetically engineering the nicotine content and plant defence in tobacco plants.