Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

Transcriptomic analysis of regulating the growth and development of tomato seedlings by the crosstalk between JA and TOR signaling

KEY MESSAGE

Transcription factors MYB, WRKY, bHLH, bZIP and NAC were identified as key candidate genes for JA and TOR regulation of tomato seedling growth and development. Jasmonic acid (JA) and Target of Rapamycin (TOR) signaling pathways interact to regulate plant growth, development, and stress responses. In this study, transcriptomic and weighted gene co-expression network analysis (WGCNA) were conducted on tomato wild-type (WT) and spr2 mutant lines treated with the TOR inhibitor RAP and activator MHY1485. We identified key roles of MAPK kinase and ethylene signaling in mediating JA-TOR interaction. Core transcription factors, including MYB, WRKY, bHLH, bZIP, and NAC, were highlighted as central regulators within the interaction between JA and TOR signaling network. These findings advance our understanding of how JA and TOR signaling coordinate plant growth and stress adaptation.

Identification and characterization of the TmSnRK2 family proteins related to chicoric acid biosynthesis in Taraxacum mongolicum

BACKGROUND

Taraxacum mongolicum is rich in phenolic acids and is widely utilized in food and medicine globally. Our previous research demonstrated that the abscisic acid (ABA) hormone significantly enhances chicoric acid accumulation in T. mongolicum. SNF1-related protein kinase 2s (SnRK2s) are extensively involved in ABA signaling and have the potential to regulate the biosynthesis of phenolic acids.

RESULTS

In this study, liquid chromatography-mass spectrometry (LC-MS) and transcriptomic analyses revealed that the TmbZIP1-Tm4CL1 pathway plays a crucial role in the transcriptional regulation of chicoric acid biosynthesis. Seven TmSnRK2s were identified in T. mongolicum and classified into three groups. Analysis of the TmSnRK2s promoters (2000 bp in length) indicated that the three most prevalent stress-related elements were ABA, methyl jasmonate (MeJA), and light. ABA treatments (0 h, 2 h, 4 h, 8 h, and 24 h) showed that all seven TmSnRK2s were significantly modulated by ABA, with the exception of SnRK2.7. TmSnRK2.2, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 were localized in both the cytoplasm and nucleus, whereas TmSnRK2.1 and TmSnRK2.5 were exclusively observed in the cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays indicated that TmSnRK2.1, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 interact with TmbZIP1. The motifs 'Q(S/G)(V/D)(D/E)(I/L)××I(I/V)×EA' and 'D×(D/ED××D)' are identified as the core sites that facilitate the binding of TmSnRK2s to TmbZIP1. Dual-luciferase reporter assays demonstrated that TmSnRK2.3 and TmSnRK2.6 enhance the stability of TmbZIP1 binding to proTm4CL1.

CONCLUSION

These findings enhance our understanding of the specific roles of certain members of the TmSnRK2 family in the biosynthesis pathway of chicoric acid.

Genomic signatures of SnRKs highlighted conserved evolution within orchids and stress responses through ABA signaling in the Cymbidium ensifolium

Sucrose non-fermenting 1-related protein kinases (SnRKs) are crucial for modulating plant responses to abiotic stresses, linking metabolism with stress signaling pathways. Investigating the roles and stress responses of SnRKs in plants paves the way for developing stress-tolerant strategies in orchid species. Here, 362 SnRK members were identified from nine current orchid genomes, highlighting the conservation of these genes in evolution. Among these, 33 CeSnRKs were found across 20 chromosomes of C. ensifolium genome. Multiple duplication events increased the complexity of CeSnRKs during independent evolution. Moreover, distinct functional domains beyond the kinase domain differentiated the subfamilies. These multi-copy members existed tissue specific expressions falling into 6 main trends, especially CeSnRK1, CeCIPK9, CeCIPK23 displayed a strict floral expression. ABA-related elements were enriched in the promoters of CeSnRKs, and stress-related miRNA binding sites were identified on partial CeSnRKs. Consequently, most CeSnRKs exhibited up-regulated expression during ABA treatment. Several genes, such as CeSnRK2.1 and CeCIPK28 involved growth and development at different times and various tissues. The up-regulation of SnRK2.1, along with high expression of SnRK1 and CIPK27 under drought stress, and the differential expression patterns of CeSnRKs under cold stress, underscore the involvement of CeSnRK genes in different stress responses. Additionally, the diverse interactions of CeSnRKs with proteins highlighted a multifaceted functional network.These findings offer valuable insights for the future functional characterization formation of CeSnRKs and the adaptive evolution of genes in orchids.

Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2

Abiotic stresses are a significant constraint to plant production globally. Identifying stress-related genes can aid in the development of stress-tolerant elite genotypes and facilitate trait and crop manipulation. The primary aim of this study was to conduct whole transcriptome analyses of the salt-tolerant faba bean genotype, Hassawi-2, under different durations of salt stress (6 h, 12 h, 24 h, 48 h, and 72 h) at the early vegetative stage, to better understand the molecular basis of salt tolerance. After de novo assembly, a total of 140,308 unigenes were obtained. The up-regulated differentially expressed genes (DEGs) were 2380, 2863, 3057, 3484, and 4820 at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. Meanwhile, 1974, 3436, 2371, 3502, and 5958 genes were downregulated at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. These DEGs encoded various regulatory and functional proteins, including kinases, plant hormone proteins, transcriptional factors (TFs) basic helix-loop-helix (bHLH), Myeloblastosis (MYB), and (WRKY), heat shock proteins (HSPs), late embryogenesis abundant (LEA) proteins, dehydrin, antioxidant enzymes, and aquaporin proteins. This suggests that the faba bean genome possesses an abundance of salinity resistance genes, which trigger different adaptive mechanisms under salt stress. Some selected DEGs validated the RNA sequencing results, thus confirming similar gene expression levels. This study represents the first transcriptome analysis of faba bean leaves subjected to salinity stress offering valuable insights into the mechanisms governing salt tolerance in faba bean during the vegetative stage. This comprehensive investigation enhances our understanding of precise gene regulatory mechanisms and holds promise for the development of novel salt-tolerant faba bean salt-tolerant cultivars.

The Role of GmSnRK1-GmNodH Module in Regulating Soybean Nodulation Capacity

SnRK1 protein kinase plays hub roles in plant carbon and nitrogen metabolism. However, the function of SnRK1 in legume nodulation and symbiotic nitrogen fixation is still elusive. In this study, we identified GmNodH, a putative sulfotransferase, as an interacting protein of GmSnRK1 by yeast two-hybrid screen. The qRT-PCR assays indicate that GmNodH gene is highly expressed in soybean roots and could be induced by rhizobial infection and nitrate stress. Fluorescence microscopic analyses showed that GmNodH was colocalized with GsSnRK1 on plasma membrane. The physical interaction between GmNodH and GmSnRK1 was further verified by using split-luciferase complementary assay and pull-down approaches. In vitro phosphorylation assay showed that GmSnRK1 could phosphorylate GmNodH at Ser193. To dissect the function and genetic relationship of GmSnRK1 and GmNodH in soybean, we co-expressed the wild-type and mutated GmSnRK1 and GmNodH genes in soybean hairy roots and found that co-expression of GmSnRK1/GmNodH genes significantly promoted soybean nodulation rates and the expression levels of nodulation-related GmNF5α and GmNSP1 genes. Taken together, this study provides the first biological evidence that GmSnRK1 may interact with and phosphorylate GmNodH to synergistically regulate soybean nodulation.

Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress

BACKGROUND

Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play crucial roles in plant signaling pathways and stress adaptive responses by activating protein phosphorylation pathways. However, there have been no comprehensive studies of the SnRK gene family in the widely planted salt-tolerant tree species Casuarina equisetifolia. Here, we comprehensively analyze this gene family in C. equisetifolia using genome-wide identification, characterization, and profiling of expression changes in response to salt stress.

RESULTS

A total of 26 CeqSnRK genes were identified, which were divided into three subfamilies (SnRK1, SnRK2, and SnRK3). The intron-exon structures and protein‑motif compositions were similar within each subgroup but differed among groups. Ka/Ks ratio analysis indicated that the CeqSnRK family has undergone purifying selection, and cis-regulatory element analysis suggested that these genes may be involved in plant development and responses to various environmental stresses. A heat map was generated using quantitative real‑time PCR (RT-qPCR) data from 26 CeqSnRK genes, suggesting that they were expressed in different tissues. We also examined the expression of all CeqSnRK genes under exposure to different salt concentrations using RT-qPCR, finding that most CeqSnRK genes were regulated by different salt treatments. Moreover, co-expression network analysis revealed synergistic effects among CeqSnRK genes.

CONCLUSIONS

Several CeqSnRK genes (CeqSnRK3.7, CeqSnRK3.16, CeqSnRK3.17) were up-regulated following salt treatment. Among them, CeqSnRK3.16 expression was significantly up-regulated under various salt treatments, identifying this as a candidate gene salt stress tolerance gene. In addition, CeqSnRK3.16 showed significant expression change correlations with multiple genes under salt stress, indicating that it might exhibit synergistic effects with other genes in response to salt stress. This comprehensive analysis will provide a theoretical reference for CeqSnRK gene functional verification and the role of these genes in salt tolerance.

Genome-wide identification and expression analysis of mitogen-activated protein kinase (MAPK) genes in response to salinity stress in channel catfish (Ictalurus punctatus)

The mitogen-activated protein kinase (MAPK) gene family has been systematically described in several fish species, but less so in channel catfish (Ictalurus punctatus), which is an important global aquaculture species. In this study, 16 MAPK genes were identified in the channel catfish genome and classified into three subfamilies based on phylogenetic analysis, including six extracellular signal regulated kinase (ERK) genes, six p38-MAPK genes and four C-Jun N-terminal kinase (JNK) genes. All MAPK genes were distributed unevenly across 10 chromosomes, of which three (IpMAPK8, IpMAPK12 and IpMAPK14) underwent teleost-specific whole genome duplication during evolution. Gene expression profiles in channel catfish during salinity stress were analysed using transcriptome sequencing and qRT-PCR (quantitative reverse transcription PCR). Results from reads per kilobase million (RPKM) analysis showed IpMAPK13, IpMAPK14a and IpMAPK14b genes were differentially expressed when compared with other genes between treatment and control groups. Furthermore, three of these genes were validated by qRT-PCR, of which IpMAPK14a expression levels were significantly upregulated in treatment groups (high and low salinity) when compared with the control group, with the highest expression levels in the low salinity group (P < 0.05). Therefore, IpMAPK14a may have important response roles to salinity stress in channel catfish.

Barley GRIK1-SnRK1 kinases subvert a viral virulence protein to upregulate antiviral RNAi and inhibit infection

Viruses often usurp host machineries for their amplification, but it remains unclear if hosts may subvert virus proteins to regulate viral proliferation. Here, we show that the 17K protein, an important virulence factor conserved in barley yellow dwarf viruses (BYDVs) and related poleroviruses, is phosphorylated by host GRIK1‐SnRK1 kinases, with the phosphorylated 17K (P17K) capable of enhancing the abundance of virus‐derived small interfering RNAs (vsiRNAs) and thus antiviral RNAi. Furthermore, P17K interacts with barley small RNA‐degrading nuclease 1 (HvSDN1) and impedes HvSDN1‐catalyzed vsiRNA degradation. Additionally, P17K weakens the HvSDN1‐HvAGO1 interaction, thus hindering HvSDN1 from accessing and degrading HvAGO1‐carried vsiRNAs. Importantly, transgenic expression of 17K phosphomimetics (17K^5D), or genome editing of SDN1, generates stable resistance to BYDV through elevating vsiRNA abundance. These data validate a novel mechanism that enhances antiviral RNAi through host subversion of a viral virulence protein to inhibit SDN1‐catalyzed vsiRNA degradation and suggest new ways for engineering BYDV‐resistant crops.

Jasmonate: A hormone of primary importance for plant metabolism

Over the years, jasmonates (JAs) have become recognized as one of the main plant hormones that regulate stress responses by activating defense programs and the production of specialized metabolites. High JA levels have been associated with reduced plant growth, supposedly as a result of the reallocation of carbon sources from primary growth to the biosynthesis of defense compounds. Recent advances suggest however that tight regulatory networks integrate several sensing pathways to steer plant metabolism, and thereby drive the trade-off between growth and defense. In this review, we discuss how JA influences primary metabolism and how it is connected to light-regulated processes, nutrient sensing and energy metabolism. Finally, we speculate that JA, in a conceptual parallelism with adrenaline for humans, overall boosts cellular processes to keep up with an increased metabolic demand during harsh times.

The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling

After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.