Search Results (61)

Tubby-like proteins (TLPs) are essential multifunctional transcription factors in plants that significantly influence plant growth and development, signal transduction, and adaptation to environmental stress. Despite their importance, there is limited knowledge of the identification and functional roles of the TLP gene family in the common bean. In this study, we identified the PvTLP gene family, which consists of 10 PvTLP genes distributed unevenly across seven chromosomes. Phylogenetic analysis revealed that these genes could be classified into three subfamilies (A, B, and C). All PvTLP proteins contained both conserved tubby and F-box domains, with the exception of PvTLP7, which lacks the F-box domain. Conserved motif analysis revealed that 10 PvTLP genes contained motif 1 and motif 3. Cis-acting elements analysis indicated that PvTLP genes might be involved in light, hormone, and stress responses. Synteny analysis revealed a closer phylogenetic relationship between the common bean and dicotyledons than monocotyledons. qRT-PCR analysis confirmed the significant differences in the expression of most PvTLP genes in both leaves and roots under salt and drought stresses. These findings provide valuable insights for further exploration of the molecular functions of TLPs in plant responses to various stresses and offer key candidate genes for enhancing stress resistance in the common bean through molecular breeding. Full article

YTH domain-containing proteins act as the primary readers of N⁶-methyladenosine (m⁶A), playing an important role in plant development and stress responses. However, little is known about the YTH proteins in medicinal plants. Genome-wide identification of the YTH gene family in the medicinal model plant, Salvia miltiorrhiza Bunge, identified a total of nineteen SmYTH genes from five chromosomes, with SmYTH8–SmYTH19 clustered on chromosome 8. Phylogenetic analysis showed that SmYTH proteins belong to the YTHDF category. No YTHDC members were identified. Conserved domain identification, amino acid sequence alignment, and phase separation prediction revealed that SmYTH1–SmYTH4 exhibited the characteristic m⁶A reader protein feature, containing conserved aromatic cages (WWW) capable of binding m⁶A residues. SmYTH5–SmYTH19 proteins contain a unique conserved F-box protein interaction domain that has not been reported previously. qRT-PCR analysis revealed tissue-specific patterns, with SmYTH1–SmYTH4 genes highly expressed in roots and leaves, whereas SmYTH8–SmYTH19 were mainly expressed in leaves. The results were consistent with RNA-seq data. The expression of various SmYTHs and the content of phenolic acid active ingredients were significantly altered under MeJA and SA treatments. The results provide useful information for further studies on the biological functions of m⁶A and YTH proteins in S. miltiorrhiza. Full article

Pathogens deploy various molecular mechanisms to overcome host defenses, among which glycoside hydrolases (GHs) play a critical role as virulence factors. Understanding the functional roles of these enzymes is essential for uncovering pathogen–host interactions and developing strategies for disease management. Fusarium wilt has occurred in the main Piper nigrum cultivation regions, which seriously affects the yield and quality of P. nigrum. Here, we identified and characterized FsGH28c, a GH28 family member in Fusarium solani. Its expression was significantly upregulated during the infection of black pepper (Piper nigrum) roots by F. solani cv. WN-1, indicating its potential role in pathogenicity. FsGH28c elicited cell death in Nicotiana benthamiana and modulated the expression of genes related to pathogenesis. FsGH28c exerts a positive influence on the pathogenicity of F. solani. The knockout of FsGH28c mutant strains markedly attenuated F. solani ’s virulence in black pepper plants. The knockout mutant strains decrease the ability of F. solani to utilize carbon sources. The FsGH28c deletion did not affect mycelial growth on PDA but did impact spore development. We identified a U-box protein, PnPUB35, interacting with FsGH28c using yeast two-hybrid and bimolecular fluorescence complementation assays. PnPUB35 conferred enhanced resistance to F. solani in black pepper through positive regulation. These findings suggest that FsGH28c may function as a virulence factor by modulating host immune responses through its interaction with PnPUB35. Full article

Accumulating evidence suggests that the plasma membrane-localized phosphate transporter 1 (PHT1) family plays a fundamental role in the absorption, translocation, and re-mobilization of phosphorus in plants. Buckwheat (Fagopyrum spp.) exhibits high efficiency in phosphate uptake and wide adaptability to grow in under-fertilized soils. Despite their physiological importance, a systematic analysis of PHT1 genes in buckwheat has not been conducted yet. In this study, we performed a genome-wide identification and expression profile of the PHT1 gene family in Tartary buckwheat (Fagopyrum tataricum Gaertn). A total of eleven putative PHT1 genes (FtPHT1;1 to 1;11) were identified with an uneven distribution on all the F. tataricum chromosomes except for chromosomes 2, 3, and 5. All the FtPHT1s share the conserved domain GGDYPLSATIxSE, a typical signature of PHT1 transporters. A phylogenetic analysis indicated that FtPHT1 proteins could be clustered into four distinct subgroups, well supported by the exon–intron structure, consensus motifs, and the domain architecture. A gene duplication analysis suggested that tandem duplication may largely contribute to the expansion of the FtPHT1 gene family members. In silico predictions of cis-acting elements revealed that low-phosphate-responsive elements, such as W-box, P1BS, and MBS, were enriched in the promoter regions of FtPHT1 genes. Quantitative real-time PCR assays showed differential but partially overlapping expression patterns of some FtPHT1 genes in various organs under limited Pi supply and hormone stimuli, implying that these FtPHT1 transporters may be essential for Pi uptake, translocation, and re-mobilization, possibly through signaling cross-talk between the low phosphate and hormones. These observations provide molecular insights into the FtPHT1 gene family, which paves the way to a functional analysis of FtPHT1 members in the future. Full article

SKP1 constitutes the Skp1-Cullin-F-box ubiquitin E3 ligase (SCF), which plays a role in plant growth and development and biotic and abiotic stress in ubiquitination. However, the response of the SKP1-like gene family to abiotic and biotic stresses in cotton has not been well characterized. In this study, a total of 72 SKP1-like genes with the conserved domain of SKP1 were identified in four Gossypium species. Synteny and collinearity analyses revealed that segmental duplication played a major role in the expansion of the cotton SKP1-like gene family. All SKP1-like proteins were classified into three different subfamilies via phylogenetic analysis. Furthermore, we focused on a comprehensive analysis of SKP1-like genes in G. hirsutum. The cis-acting elements in the promoter site of the GhSKP1-like genes predict their involvement in multiple hormonal and defense stress responses. The expression patterns results indicated that 16 GhSKP1-like genes were expressed in response to biotic or abiotic stresses. To further validate the role of the GhSKP1-like genes in salt stress, four GhSKP1-like genes were randomly selected for gene silencing via VIGS. The results showed that the silencing of GhSKP1-like_7A resulted in the inhibition of plant growth under salt stress, suggesting that GhSKP1-like_7A was involved in the response to salt stress. In addition, yeast two-hybrid results revealed that GhSKP1-like proteins have different abilities to interact with F-box proteins. These results provide valuable information for elucidating the evolutionary relationships of the SKP1-like gene family and aiding further studies on the function of SKP1-like genes in cotton. Full article

In this study, the drought-responsive gene HvFBX158 from barley was transferred to Arabidopsis thaliana, and overexpression lines were obtained. The phenotypic characteristics of the transgenic plants, along with physiological indicators and transcription level changes of stress-related genes, were determined under drought treatment. Under drought stress, transgenic plants overexpressing HvFBX158 exhibited enhanced drought tolerance and longer root lengths compared to wild-type plants. Additionally, malondialdehyde and hydrogen peroxide contents were significantly lower in transgenic lines, while superoxide dismutase activity was elevated. Quantitative RT-PCR showed that the expression levels of drought and stress response genes, including AtP5CS, AtDREB2A, AtGSH1, AtHSP17.8, and AtSOD, were significantly upregulated. Transcriptome analysis further confirmed that HvFBX158 regulated multiple stress tolerance pathways. In summary, the overexpression of the HvFBX158 gene enhanced drought tolerance in Arabidopsis thaliana by regulating multiple stress response pathways. This study provides a practical basis for improving drought-resistant barley varieties and lays a foundation for subsequent research on F-box family genes for stress resistance in barley. Full article

In this paper, Panax ginseng cyclophilin (PgCyP) was successfully obtained through a genetic engineering technique. A bioinformatics method was used to analyze the physicochemical properties and structure of PgCyP. The results showed that PgCyP belongs to the cyclophilin gene family. The protein encoded by the PgCyP gene contains the active site of PPIase (R62, F67, and H133) and a binding site for cyclosporine A (W128). The relative molecular weight of PgCyP is 187.11 bp; its theoretical isoelectric point is 7.67, and it encodes 174 amino acids. The promoter region of PgCyP mainly contains the low-temperature environmental stress response (LTR) element, abscisic acid-responsive cis-acting element (ABRE), and light-responsive cis-acting element (G-Box). PgCyP includes a total of nine phosphorylation sites, comprising four serine phosphorylation sites, three threonine phosphorylation sites, and two tyrosine phosphorylation sites. PgCyP was recombined and expressed in vitro, and its recombinant expression was investigated. Furthermore, it was found that the recombinant PgCyP protein could effectively inhibit the germination of Phytophthora cactorum spores and the normal growth of Phytophthora cactorum mycelia in vitro. Further experiments on the roots of susceptible Arabidopsis thaliana showed that the PgCyP protein could improve the resistance of arabidopsis to Phytophthora cactorum. The findings of this study provide a basis for the use of the PgCyP protein as a new type of green biopesticide. Full article

B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development. Full article

Nuclear factor Ys (NF-Ys) are heterotrimeric transcription factors that specifically bind to CCAAT boxes present in numerous eukaryotic promoters. In plants, NF-Y proteins consist of the following three subunits: NF-YA, NF-YB, and NF-YC, each encoded by a gene family. Accumulating evidence underscores the crucial roles of NF-Y proteins in various plant development processes and stress responses, such as embryogenesis, flowering time control, drought tolerance, and heat tolerance. Despite this, a comprehensive genome-wide overview of the NF-Y gene family in strawberries is lacking. To bridge this gap, this study was conducted to identify and characterize the NF-Ys in Fragaria vesca. The investigation revealed the presence of six NF-YA, twelve NF-YB, and five NF-YC members in F. vesca. Furthermore, a comprehensive analysis of the FveNF-Ys was performed, including their phylogenetic relationships, gene structures, chromosomal locations, and conserved domains. MiRNA target site prediction found that there were 30 miRNA target sites in 12 (52.2%) FveNF-Y genes. Additionally, the expression profiles of different tissues and developmental stages demonstrated tissue-specific expression patterns among certain members of each NF-Y subfamily. This observation suggests that specific NF-Y subfamily members may play unique roles in different tissues or stages of development. Furthermore, the transient expression assay demonstrated that three selected FveNF-Ys were localized in the nucleus. Our study represents a pioneering effort in the systemic analyses of FveNF-Y genes and will be useful in understanding the functional characterization of NF-Y genes in Fragaria species. Full article

Currently, more than 55 million people around the world suffer from dementia, and Alzheimer’s Disease and Related Dementias (ADRD) accounts for nearly 60–70% of all those cases. The spread of Alzheimer’s Disease (AD) pathology and progressive neurodegeneration in the hippocampus and cerebral cortex is strongly correlated with cognitive decline in AD patients; however, the molecular underpinning of ADRD’s causality is still unclear. Studies of postmortem AD brains and animal models of AD suggest that elevated endoplasmic reticulum (ER) stress may have a role in ADRD pathology through altered neurocellular homeostasis in brain regions associated with learning and memory. To study the ER stress-associated neurocellular response and its effects on neurocellular homeostasis and neurogenesis, we modeled an ER stress challenge using thapsigargin (TG), a specific inhibitor of sarco/endoplasmic reticulum Ca²⁺ ATPase (SERCA), in the induced pluripotent stem cell (iPSC)-derived neural stem cells (NSCs) of two individuals from our Mexican American Family Study (MAFS). High-content screening and transcriptomic analysis of the control and ER stress-challenged NSCs showed that the NSCs’ ER stress response resulted in a significant decline in NSC self-renewal and an increase in apoptosis and cellular oxidative stress. A total of 2300 genes were significantly (moderated t statistics FDR-corrected p-value ≤ 0.05 and fold change absolute ≥ 2.0) differentially expressed (DE). The pathway enrichment and gene network analysis of DE genes suggests that all three unfolded protein response (UPR) pathways, protein kinase RNA-like ER kinase (PERK), activating transcription factor-6 (ATF-6), and inositol-requiring enzyme-1 (IRE1), were significantly activated and cooperatively regulated the NSCs’ transcriptional response to ER stress. Our results show that IRE1/X-box binding protein 1 (XBP1) mediated transcriptional regulation of the E2F transcription factor 1 (E2F1) gene, and its downstream targets have a dominant role in inducing G1/S-phase cell cycle arrest in ER stress-challenged NSCs. The ER stress-challenged NSCs also showed the activation of C/EBP homologous protein (CHOP)-mediated apoptosis and the dysregulation of synaptic plasticity and neurotransmitter homeostasis-associated genes. Overall, our results suggest that the ER stress-associated attenuation of NSC self-renewal, increased apoptosis, and dysregulated synaptic plasticity and neurotransmitter homeostasis plausibly play a role in the causation of ADRD. Full article

Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits—grain protein content (GPC) and thousand kernel weight (TKW)—across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content. Full article

Self-incompatibility is a widespread genetic mechanism found in flowering plants. It plays a crucial role in preventing inbreeding and promoting outcrossing. The genes that control self-incompatibility in plants are typically determined by the S-locus female determinant factor and the S-locus male determinant factor. In the Solanaceae family, the male determinant factor is often the SLF gene. In this research, we cloned and analyzed 13 S₂-LbSLF genes from the L. barbarum genome, which are located on chromosome 2 and close to the physical location of the S-locus female determinant factor S-RNase, covering a region of approximately 90.4 Mb. The amino acid sequence identity of the 13 S₂-LbSLFs is 58.46%, and they all possess relatively conserved motifs and typical F-box domains, without introns. A co-linearity analysis revealed that there are no tandemly repeated genes in the S₂-LbSLF genes, and that there are two pairs of co-linear genes between S₂-LbSLF and the tomato, which also belongs to the Solanaceae family. A phylogenetic analysis indicates that the S₂-LbSLF members can be divided into six groups, and it was found that the 13 S₂-LbSLFs are clustered with the SLF genes of tobacco and Petunia inflata to varying degrees, potentially serving as pollen determinant factors regulating self-incompatibility in L. barbarum. The results for the gene expression patterns suggest that S₂-LbSLF is only expressed in pollen tissue. The results of the yeast two-hybrid assay showed that the C-terminal region of S₂-LbSLFs lacking the F-box domain can interact with S-RNase. This study provides theoretical data for further investigation into the functions of S₂-LbSLF members, particularly for the identification of pollen determinant factors regulating self-incompatibility in L. barbarum. Full article

Alfalfa (Medicago sativa L.) is an important forage crop worldwide, but molecular genetics and breeding research in this species are hindered by its self-incompatibility (SI). Although the mechanisms underlying SI have been extensively studied in other plant families, SI in legumes, including alfalfa, remains poorly understood. Here, we determined that self-pollinated pollen tubes could germinate on the stigma of alfalfa, grow through the style, and reach the ovarian cavity, but the ovules collapsed ~48 h after self-pollination. A transcriptomic analysis of dissected pistils 24 h after self-pollination identified 941 differently expressed genes (DEGs), including 784 upregulated and 157 downregulated genes. A gene ontology (GO) analysis showed that the DEGs were highly enriched in functions associated with the regulation of pollen tube growth and pollen germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that pentose and glucuronate interconversion, plant hormone signal transduction, the spliceosome, and ribosomes might play important roles in SI. Our co-expression analysis showed that F-box proteins, serine/threonine protein kinases, calcium-dependent protein kinases (CDPKs), bHLHs, bZIPs, and MYB-related family proteins were likely involved in the SI response. Our study provides a catalog of candidate genes for further study to understand SI in alfalfa and related legumes. Full article

F-box proteins are a large gene family in plants, and play crucial roles in plant growth, development, and stress response. To date, a comprehensive investigation of F-box family genes in peanuts, and their expression pattern in lateral branch development has not been performed. In this study, a total of 95 F-box protein family members on 18 chromosomes, named AhFBX1-AhFBX95, were identified in cultivated peanut (Arachis hypogaea L.), which were classified into four groups (Group I–IV). The gene structures and protein motifs of these peanut FBX genes were highly conserved among most FBXs. We found that significant segmental duplication events occurred between wild diploid species and the allotetraploid of peanut FBXs, and observed that AhFBXs underwent strong purifying selection throughout evolution. Cis-acting elements related to development, hormones, and stresses were identified in the promoters of AhFBX genes. In silico analysis of AhFBX genes revealed expression patterns across 22 different tissues. A total of 32 genes were predominantly expressed in leaves, pistils, and the aerial gynophore tip. Additionally, 37 genes displayed tissue-specific expression specifically at the apex of both vegetative and reproductive shoots. During our analysis of transcriptome data for lateral branch development in spreading and erect varieties, namely M130 and JH5, we identified nine deferentially expressed genes (DEGs). Quantitative real-time PCR (qRT-PCR) results further confirmed the expression patterns of these DEGs. These DEGs exhibited significant differences in their expression levels at different stages between M130 and JH5, suggesting their potential involvement in the regulation of lateral branch development. This systematic research offers valuable insights into the functional dissection of AhFBX genes in regulating plant growth habit in peanut. Full article

The F-box gene family is one of the largest gene families in plants, and it plays a crucial role in regulating plant development, reproduction, cellular protein degradation, and response to biotic and abiotic stresses. Despite their significance, a comprehensive analysis of the F-box gene family in Liriodendron chinense and other magnoliaceae species has not been reported. In this study, we report for the first time the identification of 144 full-length F-box genes in L. chinense. Based on specific domains and phylogenetic analyses, these genes were divided into 10 distinct subfamilies. We further analyzed their gene structure, conserved domain and chromosome distribution, genome-wide replication events, and collinearity. Additionally, based on GO analysis, we found that F-box genes exhibit functional specificity, with a significant proportion of them being involved in protein binding (GO:0005515), suggesting that F-box genes may play an important role in gene regulation in L. chinense. Transcriptome data and q-PCR results also showed that F-box genes are involved in the development of multiple tissues in L. chinense, regulate the somatic embryogenesis of Liriodendron hybrids, and play a pivotal role in abiotic stress. Altogether, these findings provide a foundation for understanding the biological function of F-box genes in L. chinense and other plant species. Full article