Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

Overexpressing OsNF-YB12 elevated the content of jasmonic acid and impaired drought tolerance in rice

Nuclear factor Y (NF-Y) is an evolutionarily conserved heterotrimeric transcription factor in eukaryotes. In a previous study, OsNF-YB12 was confirmed to be associated with drought tolerance using the Ecotilling method. In this study, real-time quantitative RT-PCR revealed that OsNF-YB12 was induced by various abiotic stresses and phytohormones, with expression levels differing between leaves and roots. Rice overexpressing OsNF-YB12 was more sensitive to salinity and PEG osmotic stresses at seed germination stage, as well as reduced drought tolerance at seedling stage. Notably, the accumulation of free proline and photosynthetic efficiency was significantly declined in OsNF-YB12 transgenic plants following osmotic stimuli. Transcriptomic analysis of transgenic OsNF-YB12 plants indicated that OsNF-YB12 could upregulate terpene metabolism related to defense responses and the expression levels of JAZ proteins under normal conditions, while downregulating osmotic stress-related regulatory genes under osmotic stress, in comparison to the wild type. Further analysis revealed that overexpressing OsNF-YB12 promoted JA biosynthesis and inhibit seed germination. Haplotype analysis suggested that OsNF-YB12 may have been selected during the differentiation of indica and japonica rice varieties. Therefore, this research provides a potential molecular target for exploring and harnessing the haplotype diversity of OsNF-YB12 to enhance yield stability under drought stress during rice domestication and improvement.

Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat (Triticum aestivum L.)

The NF-YA gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the NF-YA gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19 TaNF-YA genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of TaNF-YAs. Furthermore, cis-acting elements within the promoters of TaNF-YAs were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the NF-YA gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify TaNF-YAs influencing grain development. Finally, it was found that NF-YAs had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation.

Plant Nuclear Factor Y (NF-Y) Transcription Factors: Evolving Insights into Biological Functions and Gene Expansion

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.

ROS and Abiotic Stress in Plants 2.0

Climate insecurity and extreme weather events have stimulated efforts to enhance plant resilience and productivity in adverse environmental conditions [...].

Crucial Abiotic Stress Regulatory Network of NF-Y Transcription Factor in Plants

Nuclear Factor-Y (NF-Y), composed of three subunits NF-YA, NF-YB and NF-YC, exists in most of the eukaryotes and is relatively conservative in evolution. As compared to animals and fungi, the number of NF-Y subunits has significantly expanded in higher plants. The NF-Y complex regulates the expression of target genes by directly binding the promoter CCAAT box or by physical interaction and mediating the binding of a transcriptional activator or inhibitor. NF-Y plays an important role at various stages of plant growth and development, especially in response to stress, which attracted many researchers to explore. Herein, we have reviewed the structural characteristics and mechanism of function of NF-Y subunits, summarized the latest research on NF-Y involved in the response to abiotic stresses, including drought, salt, nutrient and temperature, and elaborated the critical role of NF-Y in these different abiotic stresses. Based on the summary above, we have prospected the potential research on NF-Y in response to plant abiotic stresses and discussed the difficulties that may be faced in order to provide a reference for the in-depth analysis of the function of NF-Y transcription factors and an in-depth study of plant responses to abiotic stress.

The NF-Y Transcription Factor Family in Watermelon: Re-Characterization, Assembly of ClNF-Y Complexes, Hormone- and Pathogen-Inducible Expression and Putative Functions in Disease Resistance

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor that binds to the CCAAT cis-element in the promoters of target genes and plays critical roles in plant growth, development, and stress responses. In the present study, we aimed to re-characterize the ClNF-Y family in watermelon, examine the assembly of ClNF-Y complexes, and explore their possible involvement in disease resistance. A total of 25 ClNF-Y genes (7 ClNF-YAs, 10 ClNF-YBs, and 8 ClNF-YCs) were identified in the watermelon genome. The ClNF-Y family was comprehensively characterized in terms of gene and protein structures, phylogenetic relationships, and evolution events. Different types of cis-elements responsible for plant growth and development, phytohormones, and/or stress responses were identified in the promoters of the ClNF-Y genes. ClNF-YAs and ClNF-YCs were mainly localized in the nucleus, while most of the ClNF-YBs were localized in the cytoplasm of cells. ClNF-YB5, -YB6, -YB7, -YB8, -YB9, and -YB10 interacted with ClNF-YC2, -YC3, -YC4, -YC5, -YC6, -YC7, and -YC8, while ClNF-YB1 and -YB3 interacted with ClNF-YC1. A total of 37 putative ClNF-Y complexes were identified, e.g., ClNF-YA1, -YA2, -YA3, and -YA7 assembled into 13, 8, 8, and 8 ClNF-Y complexes with different ClNF-YB/-YC heterodimers. Most of the ClNF-Y genes responded with distinct expression patterns to defense hormones such as salicylic acid, methyl jasmonate, abscisic acid, and ethylene precursor 1-aminocyclopropane-1-carboxylate, and to infection by the vascular infecting fungus Fusarium oxysporum f. sp. niveum. Overexpression of ClNF-YB1, -YB8, -YB9, ClNF-YC2, and -YC7 in transgenic Arabidopsis resulted in an earlier flowering phenotype. Overexpression of ClNF-YB8 in Arabidopsis led to enhanced resistance while overexpression of ClNF-YA2 and -YC2 resulted in decreased resistance against Botrytis cinerea. Similarly, overexpression of ClNF-YA3, -YB1, and -YC4 strengthened resistance while overexpression of ClNF-YA2 and -YB8 attenuated resistance against Pseudomonas syringae pv. tomato DC3000. The re-characterization of the ClNF-Y family provides a basis from which to investigate the biological functions of ClNF-Y genes in respect of growth, development, and stress response in watermelon, and the identification of the functions of some ClNF-Y genes in disease resistance enables further exploration of the molecular mechanism of ClNF-Ys in the regulation of watermelon immunity against diverse pathogens.

Five NUCLEAR FACTOR-Y subunit B genes in rapeseed (Brassica napus) promote flowering and root elongation in Arabidopsis

Heterologous expression of BnNF-YB2, BnNF-YB3, BnNF-YB4, BnNF-YB5, or BnNF-YB6 from rapeseed promotes the floral process and also affects root development in Arabidopsis. The transcriptional regulator NUCLEAR FACTOR-Y (NF-Y) is a heterotrimeric complex composed of NF-YA, NF-YB, and NF-YC proteins and is ubiquitous in yeast, animal, and plant systems. In this study, we found that five NF-YB proteins from rapeseed (Brassica napus), including BnNF-YB2, BnNF-YB3, BnNF-YB4, BnNF-YB5, and BnNF-YB6 (BnNF-YB2/3/4/5/6), all function in photoperiodic flowering and root elongation. Sequence alignment and phylogenetic analysis showed that BnNF-YB2/3 and BnNF-YB4/5/6 were clustered with Arabidopsis AtNF-YB2 and AtNF-YB3, respectively, implying that these NF-YBs are evolutionarily and functionally conserved. In support of this hypothesis, the heterologous expression of individual BnNF-YB2, 3, 4, 5, or 6 in Arabidopsis promoted early flowering under a long-day photoperiod. Further analysis suggested that BnNF-YB 2/3/4/5/6 elevated the expression of key downstream flowering time genes including CO, FT, LFY and SOC1. Promoter-GUS fusion analysis showed that the five BnNF-YBs were expressed in a variety of tissues at various developmental stages and GFP fusion analysis revealed that all BnNF-YBs were localized to the nucleus. In addition, we demonstrated that the heterologous expression of individual BnNF-YB2/3/4/5/6 in Arabidopsis promoted root elongation and increased the number of root tips formed under both normal and treatment with simulators of abiotic stress conditions.

Transcriptome profiling revealed salt stress-responsive genes in Lilium pumilum bulbs

Lilium pumilum is an important ornamental, culinary and medicinal bulbous plants with salt tolerance. However, salt tolerance of lily, particularly the bulb, has been studied relatively little, which brings challenges to the cultivation of lily varieties with high salt tolerance. Here, we performed transcriptome sequencing on the bulb organs of L. pumilum under salt stress treatment, analyzed differential gene expressed levels and then identified several key genes associated with salt stress tolerance at genome-wide scale. For the first time, we revealed the obvious response against salt stress for L. pumilum bulb organs, while distinct from those for root organs. Several key genes obtained through transcriptome analysis and DEG screening include NF-YB3 transcription factor, metallothionein type 2 protein, vicilin like seed storage protein and bidirectional sugar transporter SWEET14. Rather than typical ROS scavengers like superoxide dismutase, peroxidase, and glutathione transferase, non-typical ROS scavengers such as the metallothionein type 2 protein, and vicilin like seed storage protein were upregulated in our work. The bidirectional sugar transporter SWEET14 protein and the hormone signaling proteins such as E3-ubiquitin protein ligases, PYL4 and protein phosphatase 2C were also upregulated, suggesting the role of sugars and hormones in the bulb organ responses to salt stress. Co-expression analysis of the DEGs further confirmed that NF-YB3 transcription factor acted as a hub gene, suggesting that salt stress can promote flowering of L. pumilum. Taken together, we identified important candidate genes associated with salt tolerance of the L. pumilum bulb organs, which may provide the excellent basis for further in-depth salt tolerance mechanisms of the lily bulbs.

Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus × canescens

The NF-YA gene family is a class of conserved transcription factors that play important roles in plant growth and development and the response to abiotic stress. Poplar is a model organism for studying the rapid growth of woody plants that need to consume many nutrients. However, studies on the response of the NF-YA gene family to nitrogen in woody plants are limited. In this study, we conducted a systematic and comprehensive bioinformatic analysis of the NF-YA gene family based on Populus × canescens genomic data. A total of 13 PcNF-YA genes were identified and mapped to 6 chromosomes. According to the amino acid sequence characteristics and genetic structure of the NF-YA domains, the PcNF-YAs were divided into five clades. Gene duplication analysis revealed five pairs of replicated fragments and one pair of tandem duplicates in 13 PcNF-YA genes. The PcNF-YA gene promoter region is rich in different cis-acting regulatory elements, among which MYB and MYC elements are the most abundant. Among the 13 PcNF-YA genes, 9 contained binding sites for P. × canescens miR169s. In addition, RT-qPCR data from the roots, wood, leaves and bark of P. × canescens showed different spatial expression profiles of PcNF-YA genes. Transcriptome data and RT-qPCR analysis showed that the expression of PcNF-YA genes was altered by treatment with different nitrogen forms. Furthermore, the functions of PcNF-YA genes in transgenic poplar were analyzed, and the potential roles of PcNF-YA genes in the response of poplar roots to different nitrogen forms were revealed, indicating that these genes regulate root growth and development.

Overexpression of MsRCI2D and MsRCI2E Enhances Salt Tolerance in Alfalfa (Medicago sativa L.) by Stabilizing Antioxidant Activity and Regulating Ion Homeostasis

Rare cold-inducible 2 (RCI2) genes from alfalfa (Medicago sativa L.) are part of a multigene family whose members respond to a variety of abiotic stresses by regulating ion homeostasis and stabilizing membranes. In this study, salt, alkali, and ABA treatments were used to induce MsRCI2D and MsRCI2E expression in alfalfa, but the response time and the expression intensity of the MsRCI2D,-E genes were different under specific treatments. The expression intensity of the MsRCI2D gene was the highest in salt- and alkali-stressed leaves, while the MsRCI2E gene more rapidly responded to salt and ABA treatment. In addition to differences in gene expression, MsRCI2D and MsRCI2E differ in their subcellular localization. Akin to MtRCI2D from Medicago truncatula, MsRCI2D is also localized in the cell membrane, while MsRCI2E is different from MtRCI2E, localized in the cell membrane and the inner membrane. This difference might be related to an extra 20 amino acids in the C-terminal tail of MsRCI2E. We investigated the function of MsRCI2D and MsRCI2E proteins in alfalfa by generating transgenic alfalfa chimeras. Compared with the MsRCI2E-overexpressing chimera, under high-salinity stress (200 mmol·L-1 NaCl), the MsRCI2D-overexpressing chimera exhibited a better phenotype, manifested as a higher chlorophyll content and a lower MDA content. After salt treatment, the enzyme activities of SOD, POD, CAT, and GR in MsRCI2D- and -E-overexpressing roots were significantly higher than those in the control. In addition, after salt stress, the Na+ content in MsRCI2D- and -E-transformed roots was lower than that in the control; K+ was higher than that in the control; and the Na+/K+ ratio was lower than that in the control. Correspondingly, H+-ATPase, SOS1, and NHX1 genes were significantly up-regulated, and the HKT gene was significantly down-regulated after 6 h of salt treatment. MsRCI2D was also found to regulate the expression of the MsRCI2B and MsRCI2E genes, and the MsRCI2E gene could alter the expression of the MsRCI2A, MsRCI2B, and MsRCI2D genes. MsRCI2D- and -E-overexpressing alfalfa was found to have higher salt tolerance, manifested as improved activity of antioxidant enzymes, reduced content of reactive oxygen species, and sustained Na+ and K+ ion balance by regulating the expression of the H+-ATPase, SOS1, NHX1, HKT, and MsRCI2 genes.

Overexpression of an NF-YC2 gene confers alkali tolerance to transgenic alfalfa (Medicago sativa L.)

Alkaline stress severely limits plant growth and yield worldwide. NF-YC transcription factors (TFs) respond to abiotic stress by activating gene expression. However, the biological function of NF-YC TFs in alfalfa (Medicago sativa L.) is not clear. In our study, an NF-YC2 gene was identified and transgenic plants were obtained by constructing overexpression vector and cotyledon node transformation system in alfalfa. The open reading frame of MsNF-YC2 is 879 bp with 32.4 kDa molecular mass. MsNF-YC2 showed tissue expression specificity and was induced by a variety of abiotic stresses including drought, salt, and alkali stress in alfalfa. Under alkali stress treatment, transgenic plants exhibited higher levels of antioxidant enzyme activities and proline (Pro), correlating with a lower levels of hydrogen peroxide (H₂O₂), superoxide anion (O₂ ^-) compared with wild-type (WT) plants. Transcriptomic results showed that overexpression of MsNF-YC2 regulated the expression of phytohormone signal transduction and photosynthesis-related genes under normal and alkaline stress treatments. These results suggest that the MsNF-YC2 gene plays crucial role enhance alkali adaptation abilities in alfalfa.

Nitrogen Assimilation Related Genes in Brassicanapus: Systematic Characterization and Expression Analysis Identified Hub Genes in Multiple Nutrient Stress Responses

Nitrogen (N) is an essential macronutrient for plants. However, little is known about the molecular regulation of N assimilation in Brassica napus, one of the most important oil crops worldwide. Here, we carried out a comprehensive genome-wide analysis of the N assimilation related genes (NAGs) in B. napus. A total of 67 NAGs were identified encoding major enzymes involved in N assimilation, including asparagine synthetase (AS), glutamate dehydrogenase (GDH), glutamine oxoglutarate aminotransferase (GOGAT), glutamine synthetase (GS), nitrite reductase (NiR), nitrate reductase (NR). The syntenic analysis revealed that segmental duplication and whole-genome duplication were the main expansion pattern during gene evolution. Each NAG family showed different degrees of differentiation in characterization, gene structure, conserved motifs and cis-elements. Furthermore, diverse responses of NAG to multiple nutrient stresses were observed. Among them, more NAGs were regulated by N deficiency and ammonium toxicity than by phosphorus and potassium deprivations. Moreover, 12 hub genes responding to N starvation were identified, which may play vital roles in N utilization. Taken together, our results provide a basis for further functional research of NAGs in rapeseed N assimilation and also put forward new points in their responses to contrasting nutrient stresses.