Search Results (60)

NF-Y transcriptional regulators play crucial roles in diverse biological processes in plants, primarily through the formation of NF-Y complexes that bind to specific DNA motifs. These complexes modulate the expression of downstream genes, which influence plant development and growth. In our research, the function of the NF-Y family C subunit member SlNF-YC9 gene in tomato was investigated with the CRISPR/Cas9 method. In contrast to the WT (wild type), the mutant CR-SlNF-YC9 exhibited a prominent protrusion at the fruit tip. The quantitative PCR analysis displayed that the transcription levels of genes associated with auxin transport (PIN4, PIN5, and PIN9) as well as auxin response genes (ARF7 and LAX3) were enhanced in the CR-SlNF-YC9 fruits than in the WT. Analysis of dual-luciferase reporter and EMSA assays showed that the SlNF-YC9-YB13b-YA7a trimer specifically binds the FUL2 promoter and represses its expression. In conclusion, our results suggest that SlNF-YC9 is crucial in influencing tomato fruit shape by the formation of NF-Y heterotrimeric complexes. Full article

The CONSTANS-like (COL) gene family plays critical roles in plant growth, development, stress responses, and light signal transduction. However, its functions in peanut (Arachis hypogaea) remain poorly understood. In this study, we identified 18 AhCOL genes in the peanut genome, all localized in the nucleus. Phylogenetic analysis classified these genes into three subfamilies, with Group I containing eight members and Groups II and III each comprising five. Conserved domain analysis revealed that all AhCOL proteins possess at least one B-box and one CCT domain. Most of the AhCOL members in peanuts contain a large number of ABA and MeJA elements. Additionally, some members have low-temperature response elements, anaerobic induction, circadian control, and defense stress elements. Expression profiling indicated that most AhCOL genes are abundantly expressed in leaves, flowers, and fruit needles. Notably, genes such as AhCOL4, AhCOL8, AhCOL13, and AhCOL14 were upregulated under light induction and mechanical stress, highlighting their involvement in pod development. AhCOL1 interacts with AhNF-YC1, while AhCOL3 interacts with both AhNF-YC1 and AhCOP1 proteins. This study identifies key AhCOL genes implicated in light and mechanical stress responses, offering insights into their potential roles in peanut flowering and abiotic stress tolerance. Full article

The nuclear factor Y (NF-Y) transcription factor family identified in plant organisms consists of NF-YA, NF-YB, and NF-YC subunits, known for their pivotal role in regulating plant growth, development, and responses to environmental stress. Despite extensive studies on the NF-Y gene family across various species, the understanding of the NF-Y gene family in Eucalyptus is incomplete. This study aimed to identify 31 EgrNF-Y genes (7 EgrNF-YA, 16 EgrNF-YB, and 8 EgrNF-YC) in Eucalyptus grandis, all displaying conserved core regions. The chromosome distribution analysis showed that these genes were unevenly distributed on 11 chromosomes. The protein interaction analysis revealed EgrNF-YA1/A4/A6 as central within the EgrNF-Y protein network, interacting extensively with other EgrNF-Y proteins. Prediction of promoter cis-elements suggested that the expression of EgrNF-Y genes may be affected by various hormonal and abiotic stresses. Tissue-specific expression patterns indicated the widespread presence of all 30 EgrNF-Y genes across different tissues. EgrNF-YB1 and EgrNF-YB11 are implicated in regulating E. grandis flowering, whereas the upregulated expression of EgrNF-YB6/B11/B13 under phosphorus deficiency is involved in phosphorus absorption and utilization. This study lays a foundation for further understanding of the evolutionary diversity of the NF-Y gene family and serves as a reference for future studies in woody plants. Full article

The nuclear factor Y (NF-Y) transcription factor is widely involved in various plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress responses. This study presents a comprehensive genome-wide identification and expression profile of transcription factors NF-YB and NF-YC in Pinus koraiensis. Eight NF-YB and seven NF-YC transcription factors were identified through bioinformatics analysis, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. We evaluate the expression patterns of NF-YB/C genes in various tissues and somatic embryo maturation processes through the transcriptomics of ABA-treated tissues from multiple nutritional tissues, reproductive tissues, and somatic embryo maturation processes. The Leafy cotyledon1 (LEC1) gene belongs to the LEC1-type gene in the NF-YB family, numbered PkNF-YB7. In this study, we characterized the function of PkLEC1 during somatic embryonic development using genetic transformation techniques. The results indicate that PkNF-YB/C transcription factors are involved in the growth and development of nutritional tissues and reproductive organs, with specific high expression in PkNF-YB7 embryogenic callus, somatic embryos, zygotic embryos, and macropores. Most PkNF YB/C genes do not respond to ABA treatment during the maturation culture process. Compared with the absence of ABA, PkNF-YB8 was up-regulated in ABA treatment for one week (4.1 times) and two weeks (11.6 times). However, PkNF-YC5 was down-regulated in both one week (0.6 times) and two weeks (0.36 times) of culture, but the down-regulation trend was weakened in tissues treated with ABA (0.72–0.83 times). In addition, the promoter of PkNF YB/Cs was rich in elements that respond to various plant hormones, indicating their critical role in hormone pathways. The overexpression of PkLEC1 stimulated the generation of early somatic embryos from callus tissue with no potential for embryogenesis, enhancing the somatic embryogenesis ability of P. koraiensis callus tissue. Full article

Color variation in plant leaves has a significant impact on their photosynthesis and plant growth. Camellia chekiangoleosa yellow-leaf mutants are ideal materials for studying the mechanisms of pigment synthesis and photosynthesis, but their mechanism of leaf variation is not clear. We systematically elucidated the intrinsic causes of leaf yellowing in the new Camellia chekiangoleosa variety ‘Diecui Liuji’ in terms of changes in its cell structure, pigment content, and transcript levels. This study indicates that the incomplete structure of chloroplast-like vesicles, the decrease in blue-green chlorophyll a, and the increase in yellow-green chlorophyll b in yellowing leaves are the direct causes of yellowing-leaf formation. The high expression of genes that catalyze the degradation of chlorophyll a (PAO and RCCR) and its conversion to chlorophyll b (CAO) in yellowing leaves leads to a decrease in the chlorophyll a content, while the low expression of CLH genes is the main reason for the increase in the chlorophyll b content. We also found transcription factors such as ERF, E2F, WRKY, MYB, TPC, TGA, and NFYC may regulate their expression. RT-qPCR assays of 12 DEGs confirm the RNA-seq results. This study will provide a foundation for investigating the transcriptional and regulatory mechanisms of leaf color changes. Full article

Saline–alkali environments restrict soybean production in China. Wild soybean genes can be used to improve the alkaline tolerance of cultivated soybean in molecular breeding. The expansin protein family promotes cell wall expansion. In this study, the relative expression levels of expansin family genes in wild soybean treated with 50 mM NaHCO₃ were measured at 0, 3, 6, and 12 h, and the relative expression of GsEXPA8 was found to be higher at 12 h. Wild soybean was treated with abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellic acid (GA), and jasmonic acid (JA), and GsEXPA8 was found to respond to ABA and IAA signals. Sequence analysis shows that GsEXPA8 has DPBB_EXPA and expansin domains. Subcellular localization analysis shows that GsEXPA8 was localized in the cytoplasm in protoplasts and the cell membrane or wall in tobacco, indicating that it has nuclear membrane localization signals. GsEXPA8 overexpression reduced the malondialdehyde content in transgenic plants treated with NaHCO₃ and increased peroxidase activity before treatment. After the transformation of soybean roots from hair roots, GsEXPA8 was found to be expressed in the outer root cells and promote the development of thicker, shorter roots, thereby improving the plant’s alkaline tolerance. Stable GsEXPA8 transformation improved saline alkaline tolerance via the regulation of the alkali stress-related genes GmKIN1, GmRD22, GmDnaJA6, GmNFYC1, and GmMYB14. These findings provide support for further research on alkali-tolerance regulation pathways and molecular breeding for alkali tolerance. Full article

Gene expansion is a common phenomenon in plant transcription factor families; however, the underlying molecular mechanisms remain elusive. Examples of gene expansion in transcription factors are found in all eukaryotes. One example is plant nuclear factor Y (NF-Y) transcription factors. NF-Y is ubiquitous to eukaryotes and comprises three independent protein families: NF-YA, NF-YB, and NF-YC. While animals and fungi mostly have one of each NF-Y subunit, NF-Y is greatly expanded in plants. For example, humans have one each of NF-YA, NF-YB, and NF-YC, while the model plant Arabidopsis has ten each of NF-YA, NF-YB, and NF-YC. Our understanding of the plant NF-Y, including its biological roles, molecular mechanisms, and gene expansion, has improved over the past few years. Here we will review its biological roles and focus on studies demonstrating that NF-Y can serve as a model for plant gene expansion. These studies show that NF-Y can be classified into ancestrally related subclasses. Further, the primary structure of each NF-Y contains a conserved core domain flanked by non-conserved N- and C-termini. The non-conserved N- and C-termini, under pressure for diversifying selection, may provide clues to this gene family’s retention and functional diversification following gene duplication. In summary, this review demonstrates that NF-Y expansion has the potential to be used as a model to study the gene expansion and retention of transcription factor families. Full article

Quinoa (Chenopodium quinoa) is an Andean allotetraploid pseudocereal crop with higher protein content and balanced amino acid composition in the seeds. Ammonium (NH₄⁺), a direct source of organic nitrogen assimilation, mainly transported by specific transmembrane ammonium transporters (AMTs), plays important roles in the development, yield, and quality of crops. Many AMTs and their functions have been identified in major crops; however, no systematic analyses of AMTs and their regulatory networks, which is important to increase the yield and protein accumulation in the seeds of quinoa, have been performed to date. In this study, the CqAMTs were identified, followed by the quantification of the gene expression, while the regulatory networks were predicted based on weighted gene co-expression network analysis (WGCNA), with the putative transcriptional factors (TFs) having binding sites on the promoters of CqAMTs, nitrate transporters (CqNRTs), and glutamine-synthases (CqGSs), as well as the putative TF expression being correlated with the phenotypes and activities of GSs, glutamate synthase (GOGAT), nitrite reductase (NiR), and nitrate reductase (NR) of quinoa roots. The results showed a total of 12 members of the CqAMT family with varying expressions in different organs and in the same organs at different developmental stages. Complementation expression analyses in the triple mep1/2/3 mutant of yeast showed that except for CqAMT2.2b, 11/12 CqAMTs restored the uptake of NH₄⁺ in the host yeast. CqAMT1.2a was found to mainly locate on the cell membrane, while TFs (e.g., CqNLPs, CqG2Ls, B3 TFs, CqbHLHs, CqZFs, CqMYBs, CqNF-YA/YB/YC, CqNACs, and CqWRKY) were predicted to be predominantly involved in the regulation, transportation, and assimilation of nitrogen. These results provide the functions of CqAMTs and their possible regulatory networks, which will lead to improved nitrogen use efficiency (NUE) in quinoa as well as other major crops. Full article

The nuclear factor Y (NF-Y) gene family plays important roles in regulating many of the biological processes of plants, including oil accumulation. The apricot (Prunus armeniaca) is one of the most commercially traded plants, and apricot kernel oil has a high nutritional value owing to its richness in fatty acids and bioactive compounds. However, the systematic characterization of the PaNF-Y family in the apricot and the underlying regulatory mechanisms involved in oil biosynthesis remain unclear. In this study, a total of 28 PaNF-Y members from the apricot genome were identified and divided into three subfamilies (6 PaNF-YAs, 15 PaNF-YBs, and 7 PaNF-YCs) based on phylogenetic analysis results. The types and distributions of the gene structures and conserved motifs were similar in the clustered PaNF-Ys of the same subfamily. Gene duplication analysis results revealed that segmental duplication events were important for the expansion of the PaNF-Y family. Importantly, transcriptome data analysis results showed that most genes of the PaNF-YA subfamily and PaNF-YB4 of the PaNF-YB subfamily were specifically expressed in the apricot kernel. Furthermore, highly positive correlations were observed between apricot oil content and the transcript levels of PaNF-YA2, PaNF-YA6, and PaNF-YB4. In conclusion, our results provide insights into the molecular mechanisms of the key PaNF-Y genes regulating apricot oil biosynthesis. Full article

Respiratory infections caused by RNA viruses are a major contributor to respiratory disease due to their ability to cause annual epidemics with profound public health implications. Influenza A virus (IAV) infection can affect a variety of host signaling pathways that initiate tissue regeneration with hyperplastic and/or dysplastic changes in the lungs. Although these changes are involved in lung recovery after IAV infection, in some cases, they can lead to serious respiratory failure. Despite being ubiquitously observed, there are limited data on the regulation of long-term recovery from IAV infection leading to normal or dysplastic repair represented by inflammation-to-metaplasia transition in mice or humans. To address this knowledge gap, we used integrative bioinformatics analysis with further verification in vivo to elucidate the dynamic molecular changes in IAV-infected murine lung tissue and identified the core genes (Birc5, Cdca3, Plk1, Tpx2, Prc1. Rrm2, Nusap1, Spag5, Top2a, Mcm5) and transcription factors (E2F1, E2F4, NF-YA, NF-YB, NF-YC) involved in persistent lung injury and regeneration processes, which may serve as gene signatures reflecting the long-term effects of IAV proliferation on the lung. Further analysis of the identified core genes revealed their involvement not only in IAV infection but also in COVID-19 and lung neoplasm development, suggesting their potential role as biomarkers of severe lung disease and its complications represented by abnormal epithelial proliferation and oncotransformation. Full article

Drought has increasingly affected the yield of Solanum tuberosum L. (potato) every year over the last decade, posing serious economic problems for the global agricultural industry. Therefore, it is important to research drought tolerance in plants and obtain more robust varieties of crops. The aim of the present work was to study the expression of drought-upregulated genes in drought-tolerant and drought-sensitive varieties of potato. Bioreactors were used to identify whether each variety was drought-tolerant or drought-sensitive; then, expression analysis was performed according to the morphological characteristics of the plantlets in two different media: Murashige and Skoog (MS) medium and MS medium with 20% PEG-6000 to simulate osmotic stress. Based on the quantitative parameters of six initial varieties, two varieties were selected (Gala and Aksor) for further gene expression analysis. The expression of genes commonly upregulated in drought (ER24, TAS14, DREB147315, PP2C, 102605413 and NF-YC4) was higher in the drought-tolerant variety than in the sensitive one. Therefore, the expression of these genes can be used to determine the drought tolerance of a potato variety in vitro in the early plant development stage. Moreover, comparative analysis showed that some of the targeted genes used to identify drought tolerance in this study are conserved across different plant species. Full article

Nuclear factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NF-YB, and NF-YC. This transcription factor complex binds to the CCAAT box of eukaryotic promoters, playing a crucial role in various biological processes in plants. Despite its importance, the NF-Y gene family has not been reported in the sweet potato (Ipomoea batatas) genome, an important food and energy crop. Understanding the role and function of NF-Y in sweet potatoes could provide valuable insights for genetic improvement and yield enhancement. To address this gap, our research aimed to comprehensively catalog and characterize the NF-Y genes in sweet potatoes, which we refer to as ‘IbNF-Y’, where ‘Ib’ denotes Ipomoea batatas. A total of 37 NF-Ys were identified, including 11 NF-YA, 21 NF-YB, and 5 NF-YC members, and their phylogeny, gene structure, chromosomal distribution, and conserved motifs were analyzed. Additionally, we assessed their expression patterns under salt stress in both light and dark conditions using transcriptome sequencing. Notably, we discovered that certain IbNF-Y genes showed significant changes in expression under salt stress, suggesting their potential roles in sweet potato’s adaptation to saline environments. Furthermore, our work enriches the genomics and genetic research on sweet potatoes and contributes valuable knowledge to the broader scientific community of the Convolvulaceae family. 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

The toxic metal cadmium (Cd) poses a serious threat to plant growth and human health. Populus euphratica calcium-dependent protein kinase 21 (CPK21) has previously been shown to attenuate Cd toxicity by reducing Cd accumulation, enhancing antioxidant defense and improving water balance in transgenic Arabidopsis. Here, we confirmed a protein–protein interaction between PeCPK21 and Arabidopsis nuclear transcription factor YC3 (AtNF-YC3) by yeast two-hybrid and bimolecular fluorescence complementation assays. AtNF-YC3 was induced by Cd and strongly expressed in PeCPK21-overexpressed plants. Overexpression of AtNF-YC3 in Arabidopsis reduced the Cd inhibition of root length, fresh weight and membrane stability under Cd stress conditions (100 µM, 7 d), suggesting that AtNF-YC3 appears to contribute to the improvement of Cd stress tolerance. AtNF-YC3 improved Cd tolerance by limiting Cd uptake and accumulation, activating antioxidant enzymes and reducing hydrogen peroxide (H₂O₂) production under Cd stress. We conclude that PeCPK21 interacts with AtNF-YC3 to limit Cd accumulation and enhance the reactive oxygen species (ROS) scavenging system and thereby positively regulate plant adaptation to Cd environments. This study highlights the interaction between PeCPK21 and AtNF-YC3 under Cd stress conditions, which can be utilized to improve Cd tolerance in higher plants. Full article

Zea mays (maize) is a staple food, feed, and industrial crop. Heat stress is one of the major stresses affecting maize production and is usually accompanied by other stresses, such as drought. Our previous study identified a heterotrimer complex, ZmNF-YA1-YB16-YC17, in maize. ZmNF-YA1 and ZmNF-YB16 were positive regulators of the drought stress response and were involved in maize root development. In this study, we investigated whether ZmNF-YA1 confers heat stress tolerance in maize. The nf-ya1 mutant and overexpression lines were used to test the role of ZmNF-YA1 in maize thermotolerance. The nf-ya1 mutant was more temperature-sensitive than the wild-type (WT), while the ZmNF-YA1 overexpression lines showed a thermotolerant phenotype. Higher malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation were observed in the mutant, followed by WT and overexpression lines after heat stress treatment, while an opposite trend was observed for chlorophyll content. RNA-seq was used to analyze transcriptome changes in nf-ya1 and its wild-type control W22 in response to heat stress. Based on their expression profiles, the heat stress response-related differentially expressed genes (DEGs) in nf-ya1 compared to WT were grouped into seven clusters via k-means clustering. Gene Ontology (GO) enrichment analysis of the DEGs in different clades was performed to elucidate the roles of ZmNF-YA1-mediated transcriptional regulation and their contribution to maize thermotolerance. The loss function of ZmNF-YA1 led to the failure induction of DEGs in GO terms of protein refolding, protein stabilization, and GO terms for various stress responses. Thus, the contribution of ZmNF-YA1 to protein stabilization, refolding, and regulation of abscisic acid (ABA), ROS, and heat/temperature signaling may be the major reason why ZmNF-YA1 overexpression enhanced heat tolerance, and the mutant showed a heat-sensitive phenotype. Full article