Tissue-specific expression patterns of Arabidopsis NF-Y transcription factors suggest potential for extensive combinatorial complexity

Central role of the LEAFY COTYLEDON1 transcription factor in seed development

Seed development is a complex period of the flowering plant life cycle. After fertilization, the three main regions of the seed, embryo, endosperm and seed coat, undergo a series of developmental processes that result in the production of a mature seed that is developmentally arrested, desiccated, and metabolically quiescent. These processes are highly coordinated, both temporally and spatially, to ensure the proper growth and development of the seed. The transcription factor, LEAFY COTYLEDON1 (LEC1), is a central regulator that controls several aspects of embryo and endosperm development, including embryo morphogenesis, photosynthesis, and storage reserve accumulation. Thus, LEC1 regulates distinct sets of genes at different stages of seed development. Despite its critical importance for seed development, an understanding of the mechanisms underlying LEC1's multifunctionality is only beginning to be obtained. Recent studies describe the roles of specific transcription factors and the hormones, gibberellic acid and abscisic acid, in controlling the activity and transcriptional specificity of LEC1 across seed development. Moreover, studies indicate that LEC1 acts as a pioneer transcription factor to promote epigenetic reprogramming during embryogenesis. In this review, we discuss the mechanisms that enable LEC1 to serve as a central regulator of seed development.

Overexpression of RcLEC1-B, a HAP3 transcription factor of PLB from Rosa canina, increases the level of endogenous gibberellin and alters the development of cuticle and floral organs in Arabidopsis

The HAP3 subfamily gene RcLEC1-B, was isolated from protocorm-like body (PLB) of Rosa canina, encodes 213 amino acid residues. It was shown that RcLEC1-B was specifically expressed in PLB of R. canina and its subcellular localization is in the nucleus. Overexpression of RcLEC1-B in Arabidopsis resulted in a decrease in endogenous ABA level, an increase in GA, IAA and CTK contents, and an increased number of branches. RcLEC1-B promotes the formation of spontaneous embryoids, suggesting that it may be a homolog of the Arabidopsis LEC1 gene. RcLEC1-B-OE changed the number and morphology of flower organs and resulted in open carpels and exposed ovules, along with a reduced percentage of fertile fruit. This is the first observation that overexpression of a homolog of LEC1 in Arabidopsis can lead to morphological changes in floral organs, cuticle defects, and adhesions between organs; this may result from the increased level of gibberellin in the transgenic plants.

Genome-wide identification and co-expression network analysis of nuclear factor-Y in barley revealed potential functions in salt stress

Nuclear factor-Ys (NF-Ys) were previously shown to have important regulatory impacts in different developmental and physiological process. However, in barley the function of the NF-Y genes at system levels is not well known. To identify barley NF-Ys, Arabidopsis and wheat NF-Y protein sequences were retrieved and the BLAST program along with the hidden Markov model were used. Multiple sequence alignments of identified NF-Ys were constructed using ClustalW. Expression patterns of the NF-Ys at different physiological and developmental conditions were also surveyed based on microarray datasets in public databases and subsequently co-expression network were constructed. Validation of in silico expression analysis was performed by real-time qPCR under salt stress condition. In total, 23 barley NF-Ys (8 NF-YA, 11 NF-YB and 4 NF-YC) were identified. Based on the sequence homology, the subunits of the NF-Y complex were divided into three to five groups. Structural analysis highlighted the conserved domains of HvNF-YA, HvNF-YB and HvNF-YC. Co-expression network analysis indicated the potential functions of HvNF-Ys in photosynthesis, starch biosynthesis and osmotic stress tolerance. The results of qRT-PCR also confirmed the HvNF-Ys roles in adaptation responses of barley to salt stress. We identified some potential candidate genes which could be used for improvements of cereals tolerance to salinity stress.

The General Transcription Repressor TaDr1 Is Co-expressed With TaVrn1 and TaFT1 in Bread Wheat Under Drought

The general transcription repressor, TaDr1 gene, was identified during screening of a wheat SNP database using the Amplifluor-like SNP marker KATU-W62. Together with two genes described earlier, TaDr1A and TaDr1B, they represent a set of three homeologous genes in the wheat genome. Under drought, the total expression profiles of all three genes varied between different bread wheat cultivars. Plants of four high-yielding cultivars exposed to drought showed a 2.0-2.4-fold increase in TaDr1 expression compared to controls. Less strong, but significant 1.3-1.8-fold up-regulation of the TaDr1 transcript levels was observed in four low-yielding cultivars. TaVrn1 and TaFT1, which controls the transition to flowering, revealed similar profiles of expression as TaDr1. Expression levels of all three genes were in good correlation with grain yields of evaluated cultivars growing in the field under water-limited conditions. The results could indicate the involvement of all three genes in the same regulatory pathway, where the general transcription repressor TaDr1 may control expression of TaVrn1 and TaFT1 and, consequently, flowering time. The strength of these genes expression can lead to phenological changes that affect plant productivity and hence explain differences in the adaptation of the examined wheat cultivars to the dry environment of Northern and Central Kazakhstan. The Amplifluor-like SNP marker KATU-W62 used in this work can be applied to the identification of wheat cultivars differing in alleles at the TaDr1 locus and in screening hybrids.

Identification and characterization of NF-Y gene family in walnut (Juglans regia L.)

BACKGROUND

The eukaryotic transcription factor NF-Y (which consists of NF-YA, NF-YB and NF-YC subunits) is involved in many important plant development processes. There are many reports about the NF-Y family in Arabidopsis and other plant species. However, there are no reports about the NF-Y family in walnut (Juglans regia L.).

RESULTS

Thirty-three walnut NF-Y genes (JrNF-Ys) were identified and mapped on the walnut genome. The JrNF-Y gene family consisted of 17 NF-YA genes, 9 NF-YB genes, and 7 NF-YC genes. The structural features of the JrNF-Y genes were investigated by comparing their evolutionary relationship and motif distributions. The comparisons indicated the NF-Y gene structure was both conserved and altered during evolution. Functional prediction and protein interaction analysis were performed by comparing the JrNF-Y protein structure with that in Arabidopsis. Two differentially expressed JrNF-Y genes were identified. Their expression was compared with that of three JrCOs and two JrFTs using quantitative real-time PCR (qPCR). The results revealed that the expression of JrCO2 was positively correlated with the expression of JrNF-YA11 and JrNF-YA12. In contrast, JrNF-CO1 and JrNF-YA12 were negatively correlated.

CONCLUSIONS

Thirty-three JrNF-Ys were identified and their evolutionary, structure, biological function and expression pattern were analyzed. Two of the JrNF-Ys were screened out, their expression was differentially expressed in different development periods of female flower buds, and in different tissues (female flower buds and leaf buds). Based on prediction and experimental data, JrNF-Ys may be involved in flowering regulation by co-regulate the expression of flowering genes with other transcription factors (TFs). The results of this study may make contribution to the further investigation of JrNF-Y family.

Identification, Structural Characterization and Gene Expression Analysis of Members of the Nuclear Factor-Y Family in Chickpea (Cicer arietinum L.) under Dehydration and Abscisic Acid Treatments

In plants, the Nuclear Factor-Y (NF-Y) transcription factors (TFs), which include three distinct types of NF-YA, NF-YB, and NF-YC TFs, have been identified to play key roles in the regulation of various plant growth and developmental processes under both normal and environmental stress conditions. In this work, a total of 40 CaNF-Y-encoding genes, including eight CaNF-YAs, 21 CaNF-YBs, and 11 CaNF-YCs, were identified in chickpea, and their major gene and protein characteristics were subsequently obtained using various web-based tools. Of our interest, a phylogenetically-based analysis predicted 18 CaNF-Ys (eight CaNF-YAs, seven CaNF-YBs, and three CaNF-YCs) that potentially play roles in chickpea responses to dehydration according to their close relationship with the well-characterized GmNF-Ys in soybean. These results were in good agreement with the enrichment of drought-responsive cis-regulatory motifs and expression patterns obtained from in silico analyses using publically available transcriptome data. Most of the phylogenetically predicted drought-responsive CaNF-Y genes (15 of 18) were quantitatively validated to significantly respond to dehydration treatment in leaves and/or roots, further supporting the results of in silico analyses. Among these CaNF-Y genes, the transcript levels of CaNF-YA01 and CaNF-YC10 were the most highly accumulated in leaves (by approximately eight-fold) and roots (by approximately 18-fold), respectively, by dehydration. Furthermore, 12 of the 18 CaNF-Y genes were found to be responsive to the most well-known stress hormone, namely abscisic acid (ABA), in leaves and/or roots, suggesting that these genes may act in chickpea response to dehydration in ABA-dependent manner. Taken together, our study has provided a comprehensive and fundamental information for further functional analyses of selected CaNF-Y candidate genes, ultimately leading to the improvement of chickpea growth under water-limited conditions.

NUCLEAR FACTOR-Y: still complex after all these years?

The NUCLEAR FACTOR-Y (NF-Y) families of transcription factors are important regulators of plant development and physiology. Though NF-Y regulatory roles have recently been suggested for numerous aspects of plant biology, their roles in flowering time, early seedling development, stress responses, hormone signaling, and nodulation are the best characterized. The past few years have also seen significant advances in our understanding of the mechanistic function of the NF-Y, and as such, increasingly complex and interesting questions are now more approachable. This review will primarily focus on these developmental, physiological, and mechanistic roles of the NF-Y in recent research.

Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA

Two groups of six spring bread wheat varieties with either high or low grain yield under the dry conditions of Central and Northern Kazakhstan were selected for analysis. Experiments were set up with the selected wheat varieties in controlled environments as follows: (1) slowly progressing drought imposed on plants in soil, (2) rapid dehydration of whole plants grown in hydroponics, (3) dehydration of detached leaves, and (4) ABA treatment of whole plants grown in hydroponics. Representatives of two different families of transcription factors (TFs), TaDREB5 and TaNFYC-A7, were found to be linked to yield-under-drought using polymorphic Amplifluor-like SNP marker assays. qRT-PCR revealed differing patterns of expression of these genes in the leaves of plants subjected to the above treatments. Under drought, TaDREB5 was significantly up-regulated in leaves of all high-yielding varieties tested and down-regulated in all low-yielding varieties, and the level of expression was independent of treatment type. In contrast, TaNFYC-A7 expression levels showed different responses in the high- and low-yield groups of wheat varieties. TaNFYC-A7 expression under dehydration (treatments 2 and 3) was higher than under drought (treatment 1) in all high-yielding varieties tested, while in all low-yielding varieties the opposite pattern was observed: the expression levels of this gene under drought were higher than under dehydration. Rapid dehydration of detached leaves and intact wheat plants grown in hydroponics produced similar changes in gene expression. ABA treatment of whole plants caused rapid stomatal closure and a rise in the transcript level of both genes during the first 30 min, which decreased 6 h after treatment. At this time-point, expression of TaNFYC-A7 was again significantly up-regulated compared to untreated controls, while TaDREB5 returned to its initial level of expression. These findings reveal significant differences in the transcriptional regulation of two drought-responsive and ABA-dependent TFs under slowly developing drought and rapid dehydration of wheat plants. The results obtained suggest that correlation between grain yield in dry conditions and TaNFYC-A7 expression levels in the examined wheat varieties is dependent on the length of drought development and/or strength of drought; while in the case of TaDREB5, no such dependence is observed.

Overexpression of a NF-YC Gene Results in Enhanced Drought and Salt Tolerance in Transgenic Seashore Paspalum

Seashore paspalum (Paspalum vaginatum O. Swartz) is an important warm-season turfgrass species. In this study we generated transgenic seashore paspalum overexpressing CdtNF-YC1, a nuclear factor Y transcription factor from hybrid bermudagrass (Cynodon dactylon × Cynodon transvaalensis). DNA blot hybridization and qRT-PCR analysis showed that CdtNF-YC1 was integrated into the genomes of transgenic seashore paspalum plants and expressed. Reduced relative water content (RWC) and survival rate and increased ion leakage were observed in both wild type (WT) and transgenic plants after drought stress, while transgenic plants had higher levels of RWC and survival rate and lower ion leakage than the WT. Maximal photochemical efficiency of photosystem II (F v/F m), chlorophyll concentration and survival rate were decreased after salt stress, while higher levels were maintained in transgenic plants than in WT. In addition, an increased Na+ content and decreased or unaltered K+ in leaves and roots were observed after salt treatment, while lower level of Na+ and higher levels of K+ and K+/ Na+ ratio were maintained in transgenic plants than in WT. The results indicated that overexpressing CdtNF-YC1 resulted in enhanced drought and salt tolerance in transgenic plants. Transcript levels of stress responsive genes including PvLEA3, PvP5CS1, PvABI2, and PvDREB1B were induced in response to drought and salt stress, and higher levels were observed in transgenic seashore paspalum than in WT. The results suggest that the enhanced drought and salt tolerance in transgenic seashore paspalum is associated with induction of a series of stress responsive genes as a result of overexpression of CdtNF-YC1.

Gene network of oil accumulation reveals expression profiles in developing embryos and fatty acid composition in Upland cotton

Cottonseed oil accumulated dramatically from 20 days post-anthesis (DPA) to 30 DPA in Upland cotton (Gossypium hirsutum L.). To reveal the gene network of oil accumulation and fatty acid composition in developing embryos, embryos at 10, 20 and 30 DPA in cottonseed were sampled and used for transcriptome sequencing (RNA-Seq). In total, 8629, 7891, and 12,555 differentially expressed genes (DEGs) were identified in the comparison sets of '20 DPA vs 10 DPA', '30 DPA vs 20 DPA', and '30 DPA vs 10 DPA', respectively. The gene network highlighted the dynamic expression profiles of oil accumulation in fatty acid (FA) synthesis, FA desaturation, and triacylglycerol (TAG) biosynthesis. WRI1 and NF-YB6 were suggested elite transcription factors in regulating lipid metabolism. Compared with the gene expression levels in developing seeds, GhPDAT was highly expressed and might play a more important role than GhDGAT in transforming diacylglycerol to TAG in cotton. Expression patterns of 12 FA-biosynthesis-related genes were validated by quantitative real-time PCR (qRT-PCR) method. To reveal the reason for the high content of linoleic acid (C18:2) in cottonseed oil, we carried out a comparative analysis of gene expression levels in Upland cotton, rapeseed (Brassica napus), and oleaster (Olea europaea). Compared with in rapeseed and oleaster, GhFAD2 genes were up-regulated and GhFAD3 genes down-regulated in cottonseed, taking into account the relative high amount of C18:2 but low content of linolenic acid (C18:3) in Upland cotton. The present study offers new information to interpret the mechanism of the FA biosynthesis network and to alter FA composition in cotton breeding projects.

Populus trichocarpa PtNF-YA9, A Multifunctional Transcription Factor, Regulates Seed Germination, Abiotic Stress, Plant Growth and Development in Arabidopsis

NF-YAs play important roles in abiotic stress. However, their characteristics and functions in abiotic stress of poplar, a model woody plant, have not been fully investigated. Here, the biological functions of PtNF-YA9 (Potri.011G101000), an NF-YA gene from Populus trichocarpa, were first fully investigated. PtNF-YA9 is located in the nucleus. The expression of PtNF-YA9 was reduced by mannitol, NaCl, and abscisic acid (ABA). The GUS staining of ProNF-YA9::GUS transgenic lines was also reduced by mannitol treatments. In the PtNF-YA9-overexpressed Arabidopsis (OxPtNA9), OxPtNA9 lines exhibited sensitivity to simulated drought, ABA, and salinity stress during germination stage, and growth arrest emerged at post-germination stage. These phenomena might involve the ABA signaling pathway via the regulation of ABI3, ABI4, and ABI5. At vegetative stages, OxPtNA9 lines decreased in water loss via promoting stomatal closure and displayed high instantaneous water-use efficiency (WUE) of the leaf to exhibit enhanced drought tolerance. Furthermore, OxPtNA9 lines exhibited long primary root in the half-strength Murashige-Skoog agar medium supplemented with NaCl and conferred strong tolerance in the soil under salt stress. Additionally, PtNF-YA9 exhibited dwarf phenotype, short hypocotyl, small leaf area and biomass, delayed flowering, and increased chlorophyll content. Above all, our research proposes a model in which PtNF-YA9 not only plays a key role in reducing plant growth but also can play a primary role in the mechanism of an acclimatization strategy in response to adverse environmental conditions.

GhKLCR1, a kinesin light chain-related gene, induces drought-stress sensitivity in Arabidopsis

Drought stress results in significant losses in agricultural production, and especially that of cotton. The molecular mechanisms that coordinate drought tolerance remain elusive in cotton. Here, we isolated a drought-response gene GhKLCR1, which is a close homolog of AtKLCR1, which encodes a kinesin light chain-related protein enriched with a tetratrico peptide-repeat region. A subcellular localization assay showed that GhKLCR1 is associated with the cell membrane. A tissue-specific expression profile analysis demonstrated that GhKLCR1 is a cotton root-specific gene. Further abiotic and hormonal stress treatments showed that GhKLCR1 was upregulated during abiotic stresses, especially after polyethylene glycol treatments. In addition, the glucuronidase (GUS) staining activity increased as the increment of mannitol concentration in transgenic Arabidopsis plants harboring the fusion construct P_GhKLCR1::GUS. The root lengths of 35S::GhKLCR1 lines were significantly reduced compared with that of wild type. Additionally, seed germination was strongly inhibited in 35S::GhKLCR1 lines after 300-mmol L^-1 mannitol treatments as compared with Columbia-0, indicating the sensitivity of GhKLCR1 to drought. These findings provide a better understanding of the structural, physiological and functional mechanisms of kinesin light chain-related proteins.

ZmNF-YB16 Overexpression Improves Drought Resistance and Yield by Enhancing Photosynthesis and the Antioxidant Capacity of Maize Plants

ZmNF-YB16 is a basic NF-YB superfamily member and a member of a transcription factor complex composed of NF-YA, NF-YB, and NF-YC in maize. ZmNF-YB16 was transformed into the inbred maize line B104 to produce homozygous overexpression lines. ZmNF-YB16 overexpression improves dehydration and drought stress resistance in maize plants during vegetative and reproductive stages by maintaining higher photosynthesis and increases the maize grain yield under normal and drought stress conditions. Based on the examination of differentially expressed genes between the wild-type (WT) and transgenic lines by quantitative real time PCR (qRT-PCR), ZmNF-YB16 overexpression increased the expression of genes encoding antioxidant enzymes, the antioxidant synthase, and molecular chaperones associated with the endoplasmic reticulum (ER) stress response, and improved protection mechanism for photosynthesis system II. Plants that overexpression ZmNF-YB16 showed a higher rate of photosynthesis and antioxidant enzyme activity, better membrane stability and lower electrolyte leakage under control and drought stress conditions. These results suggested that ZmNF-YB16 played an important role in drought resistance in maize by regulating the expression of a number of genes involved in photosynthesis, the cellular antioxidant capacity and the ER stress response.

Gene structure, expression pattern and interaction of Nuclear Factor-Y family in castor bean (Ricinus communis)

Nuclear Factor-Y transcription factors, which function in regulating seed development (including storage reservoir accumulation) and responding to abiotic stresses, were identified and characterized in castor bean. Nuclear Factor-Y (NF-Y) transcription factors in plants contain three subunits (NF-YA, NF-YB and NF-YC), and function as a heterodimer or heterotrimer complex in regulating plant growth, development and response to stresses. Castor bean (Ricinus communis, Euphorbiaceae) one of the most economically important non-edible oilseed crops, able to grow in diverse soil conditions and displays high tolerance to abiotic stresses. Due to increasing demands for its seed oils, it is necessary to elucidate the molecular mechanism underlying the regulation of growth and development. Based on the available genome data, we identified 25 RcNF-Y members including six RcNF-YAs, 12 RcNF-YBs and seven RcNF-YCs, and characterized their gene structures. Yeast two-hybrid assays confirmed the protein-protein interactions among three subunits. Using transcriptomic data from different tissues, we found that six members were highly or specifically expressed in endosperms (in particular, two LEC1-type members RcNF-YB2 and RcNF-YB12), implying their involvement in regulating seed development and storage reservoir accumulation. Further, we investigated the expression changes of RcNF-Y members in two-week-old seedlings under drought, cold, hot and salt stresses. We found that the expression levels of 20 RcNF-Y members tested were changed and three RcNF-Y members might function in response to abiotic stresses. This study is the first reported on genomic characterization of NF-Y transcription factors in the family Euphorbiaceae. Our results provide the basis for improved understanding of how NF-Y genes function in the regulation of seed development and responses to abiotic stresses in both castor bean and other plants in this family.

Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis

Members of the NF-YB transcription factor gene family play important roles in diverse processes related to plant growth and development, such as seed development, drought tolerance, and flowering time. However, the function of NF-YB genes in cotton remains unclear. A total of 23, 24, and 50 NF-YB genes were identified in Gossypium arboreum (G. arboreum), Gossypium raimondii (G. raimondii), and G. hirsutum, respectively. A systematic phylogenetic analysis was carried out in G. arboretum, G. raimondii, G. hirsutum, Arabidopsis thaliana, cacao, rice and, sorghum, where the 150 NF-YB genes were divided into five groups (α–ε). Of these groups, α is the largest clade, and γ contains the LEC1 type NF-YB proteins. Syntenic analyses revealed that paralogues of NF-YB genes in G. hirsutum exhibited good collinearity. Owing to segmental duplication within the A sub-genome (A_t) and D sub-genome (D_t), there was an expanded set of NF-YB genes in G. hirsutum. Furthermore, we investigated the structures of exons, introns, and conserved motifs of NF-YB genes in upland cotton. Most of the NF-YB genes had only one exon, and the genes from the same clade exhibited a similar motif pattern. Expression data show that most NF-YB genes were expressed ubiquitously, and only a few genes were highly expressed in specific tissues, as confirmed by quantitative real-time PCR (qRT-PCR) analysis. The overexpression of GhDNF-YB22 gene, predominantly expressed in embryonic tissues, indicates that GhDNF-YB22 may affect embryogenesis in cotton. This study is the first comprehensive characterization of the GhNF-YB gene family in cotton, and showed that NF-YB genes could be divided into five clades. The duplication events that occurred over the course of evolution were the major impetus for NF-YB gene expansion in upland cotton. Collectively, this work provides insight into the evolution of NF-YB in cotton and further our knowledge of this commercially important species.

Overexpression of the transcription factor NF-YC9 confers abscisic acid hypersensitivity in Arabidopsis

Nuclear factor Y (NF-Y) family proteins are involved in many developmental processes and responses to environmental cues in plants, but whether and how they regulate phytohormone abscisic acid (ABA) signaling need further studies. In the present study, we showed that over-expression of the NF-YC9 gene confers ABA hypersensitivity in both the early seedling growth and stomatal response, while down-regulation of NF-YC9 does not affect ABA response in these processes. We also showed that over-expression of the NF-YC9 gene confers salt and osmotic hypersensitivity in early seedling growth, which is likely to be directly associated with the ABA hypersensitivity. Further, we observed that NF-YC9 physically interacts with the ABA-responsive bZIP transcription factor ABA-INSENSITIVE5 (ABI5), and facilitates the function of ABI5 to bind and activate the promoter of a target gene EM6. Additionally, NF-YC9 up-regulates expression of the ABI5 gene in response to ABA. These findings show that NF-YC9 may be involved in ABA signaling as a positive regulator and likely functions redundantly together with other NF-YC members, and support the model that the NF-YC9 mediates ABA signaling via targeting to and aiding the ABA-responsive transcription factors such as ABI5.

Regulation and evolution of the interaction of the seed B3 transcription factors with NF-Y subunits

The LAFL genes (LEC2, ABI3, FUS3, LEC1) encode transcription factors that regulate different aspects of seed development, from early to late embryogenesis and accumulation of storage compounds. These transcription factors form a complex network, with members able to interact with various other players to control the switch between embryo development and seed maturation and, at a later stage in the plant life cycle, between the mature seed and germination. In this review, we first summarize our current understanding of the role of each member in the network in the light of recent advances regarding their regulation and structure/function relationships. In a second part, we discuss new insights concerning the evolution of the LAFL genes to address the more specific question of the conservation of LEAFY COTYLEDONS 2 in both dicots and monocots and the putative origin of the network. Last we examine the current major limitations to current knowledge and future prospects to improve our understanding of this regulatory network.

Activation-tagging in indica rice identifies a novel transcription factor subunit, NF-YC13 associated with salt tolerance

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor with three distinct NF-YA, NF-YB and NF-YC subunits. It plays important roles in plant growth, development and stress responses. We have reported earlier on development of gain-of-function mutants in an indica rice cultivar, BPT-5204. Now, we screened 927 seeds from 70 Ac/Ds plants for salinity tolerance and identified one activation-tagged salt tolerant DS plant (DS-16, T3 generation) that showed enhanced expression of a novel 'histone-like transcription factor' belonging to rice NF-Y subfamily C and was named as OsNF-YC13. Localization studies using GFP-fusion showed that the protein is localized to nucleus and cytoplasm. Real time expression analysis confirmed upregulation of transcript levels of OsNF-YC13 during salt treatment in a tissue specific manner. Biochemical and physiological characterization of the DS-16 revealed enhanced K+/Na+ ratio, proline content, chlorophyll content, enzymes with antioxidant activity etc. DS-16 also showed transcriptional up-regulation of genes that are involved in salinity tolerance. In-silico analysis of OsNF-YC13 promoter region evidenced the presence of various key stress-responsive cis-regulatory elements. OsNF-YC13 subunit alone does not appear to have the capacity for direct transcription activation, but appears to interact with the B- subunits in the process of transactivation.

Overexpression of StNF-YB3.1 reduces photosynthetic capacity and tuber production, and promotes ABA-mediated stomatal closure in potato (Solanum tuberosum L.)

Nuclear factor Y (NF-Y) is one of the most ubiquitous transcription factors (TFs), comprising NF-YA, NF-YB and NF-YC subunits, and has been identified and reported in various aspects of development for plants and animals. In this work, StNF-YB3.1, a putative potato NF-YB subunit encoding gene, was isolated from Solanum tuberosum by rapid amplification of cDNA ends (RACE). Overexpression of StNF-YB3.1 in potato (cv. Atlantic) resulted in accelerated onset of flowering, and significant increase in leaf chlorophyll content in field trials. However, transgenic potato plants overexpressing StNF-YB3.1 (OEYB3.1) showed significant decreases in photosynthetic rate and stomatal conductance both at tuber initiation and bulking stages. OEYB3.1 lines were associated with significantly fewer tuber numbers and yield reduction. Guard cell size and stomatal density were not changed in OEYB3.1 plants, whereas ABA-mediated stomatal closure was accelerated compared to that of wild type plants because of the up-regulation of genes for ABA signaling, such as StCPK10-like, StSnRK2.6/OST1-like, StSnRK2.7-like and StSLAC1-like. We speculate that the acceleration of stomatal closure was a possible reason for the significantly decreased stomatal conductance and photosynthetic rate.

CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer

Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter. We term this complex NF-CO. Using saturation mutagenesis, electrophoretic mobility shift assays, and RNA-sequencing profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site. CO physically interacts with the same HFD surface required for NF-YA association, as determined by mutations in NF-YB2 and NF-YC9, and tested in vitro and in vivo. The co-7 mutation in the CCT domain, corresponding to an NF-YA arginine directly involved in CCAAT recognition, abolishes NF-CO binding to DNA. In summary, a unifying molecular mechanism of CO function relates it to the NF-YA paradigm, as part of a trimeric complex imparting sequence specificity to HFD/DNA interactions. It is likely that members of the large CCT family participate in similar complexes with At-NF-YB and At-NF-YC, broadening HFD combinatorial possibilities in terms of trimerization, DNA binding specificities, and transcriptional regulation.

Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis

In plants, leaf is crucial for photosynthesis and respiration. Leaf area and quantity are important for leaf vegetables to increase biomass. The process of leaf development involves coordinated regulation among small RNAs, transcription factors and hormones. Here, we found leaf size were regulated by transcription factors NF-YA2 and NF-YA10 in Arabidopsis. NF-YA2 and NF-YA10 overexpression increased biomass accumulation through promoting leaf growth and cell expansion. NF-YA2 and NF-YA10 were expressed in SAM and leaf vasculature. Endogenous IAA content reduced by 20% and 24% in transgenic Arabidopsis plants overexpressing NF-YA2 and NF-YA10 compared to wild-type plants. Chromatin immunoprecipitation assays revealed that NF-YA2 and NF-YA10 bound directly to the cis-element CCAAT in the promoter of the YUC2, and decreased the expression of YUC2, a YUCCA family gene. The auxin transporter gene PIN1 and auxin response factor1 and 2 (ARF1 and ARF2) genes, transcriptional repressors, were downregulated. These findings showed leaf development was regulated by NF-YA2 and NF-YA10 through the auxin-signaling pathway and may provide a new insight into the genetic engineering of vegetables biomass and crop productivity.

The garlic NF-YC gene, AsNF-YC8, positively regulates non-ionic hyperosmotic stress tolerance in tobacco

To investigate the relationship between nuclear factor Y (NF-Y) and stress tolerance in garlic, we cloned a NF-Y family gene AsNF-YC8 from garlic, which was largely upregulated at dehydrate stage. Expression pattern analyses in garlic revealed that AsNF-YC8 is induced through abscisic acid (ABA) and abiotic stresses, such as NaCl and PEG. Compared with wild-type plants, the overexpressing-AsNF-YC8 transgenic tobacco plants showed higher seed germination rates, longer root length and better plant growth under salt and drought stresses. Under drought stress, the transgenic plants maintained higher relative water content (RWC), net photosynthesis, lower levels of malondialdehyde (MDA), and less ion leakage (IL) than wild-type control plants. These results indicate the high tolerance of the transgenic plants to drought stress compared to the WT. The transgenic tobacco lines accumulated less reactive oxygen species (ROS) and exhibited higher antioxidative enzyme activities compared with wild-type (WT) plants under drought stress, which suggested that the overexpression of AsNF-YC8 improves the antioxidant defense system by regulating the activities of these antioxidant enzymes, which in turn protect transgenic lines against drought stress. These results suggest that AsNF-YC8 plays an important role in tolerance to drought and salt stresses.

Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program

Seeds are one of the most significant innovations in the land plant lineage, critical to the diversification and adaptation of plants to terrestrial environments. From perspective of seed evo-devo, the most crucial developmental stage in this innovation is seed maturation, which includes accumulation of storage reserves, acquisition of desiccation tolerance, and induction of dormancy. Based on previous studies of seed development in the model plant Arabidopsis thaliana, seed maturation is mainly controlled by the LAFL regulatory network, which includes LEAFY COTYLEDON1 (LEC1) and LEC1-LIKE (L1L) of the NF-YB gene family, and ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 (LEAFY COTYLEDON2) of the B3-AFL gene family. In the present study, molecular evolution of these LAFL genes was analyzed, using representative species from across the major plant lineages. Additionally, to elucidate the molecular mechanisms of the seed maturation program, co-expression pattern analyses of LAFL genes were conducted across vascular plants. The results show that the origin of AFL gene family dates back to a common ancestor of bryophytes and vascular plants, while LEC1-type genes are only found in vascular plants. LAFL genes of vascular plants likely specify their co-expression in two different developmental phrases, spore and seed maturation, respectively, and expression patterns vary slightly across the major vascular plants lineages. All the information presented in this study will provide insights into the origin and diversification of seed plants.

Arabidopsis NF-YCs Mediate the Light-Controlled Hypocotyl Elongation via Modulating Histone Acetylation

Light is a crucial environmental signal that promotes photomorphogenesis, the developmental process with a series of light-dependent alterations for plants to adapt various external challenges. Chromatin modification has been proposed to be involved in such light-mediated growth, but the underlying mechanism is still elusive. In this study, we identified four Arabidopsis thaliana Nuclear Factor-YC homologs, NF-YC1, NF-YC3, NF-YC4, and NF-YC9 (NF-YCs), which function redundantly as repressors of light-controlled hypocotyl elongation via histone deacetylation. Obvious etiolation phenotypes are observed in NF-YCs loss-of-function mutant seedlings grown under light conditions, including significant elongated hypocotyls and fewer opened cotyledons. We found that NF-YCs interact with histone deacetylase HDA15 in the light, co-target the promoters of a set of hypocotyl elongation-related genes, and modulate the levels of histone H4 acetylation on the associated chromatins, thus repressing gene expression. In contrast, NF-YC-HDA15 complex is dismissed from the target genes in the dark, resulting in increased level of H4 acetylation and consequent etiolated growth. Further analyses revealed that transcriptional repression activity of NF-YCs on the light-controlled hypocotyl elongation partially depends on the deacetylation activity of HDA15, and loss of HDA15 function could rescue the short-hypocotyl phenotype of NF-YCs overexpression plants. Taken together, our results indicate that NF-YC1, NF-YC3, NF-YC4, and NF-YC9 function as transcriptional co-repressors by interacting with HDA15 to inhibit hypocotyl elongation in photomorphogenesis during the early seedling stage. Our findings highlight that NF-YCs can modulate plant development in response to environmental cues via epigenetic regulation.

Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes

Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes.

Many plant species flower in response to changes in day length and can be categorized depending on their requirements for long or short days. Rice has tropical origins and normally flowers in response to shortening days. However, artificial selection operated by ancient farmers or modern breeders adapted rice cultivation to several environments, including those typical of temperate regions characterized by long days during the cropping season. Modifications of the genetic network controlling flowering that are causal to such expansion have been the subject of extensive studies, but the full complement of genes that regulate it and the molecular bases of their activity remains unknown. We took advantage of germplasm cultivated in Europe—and highly adapted to flower under long days–to isolate widespread variants of the HEADING DATE 1 (Hd1) gene that limits flowering in temperate areas, and showed that such variants are non-functional and unable to prevent long day flowering. We identified the DNA changes causing the gene to be non-functional and used such mutant alleles as tools to demonstrate that Hd1 can bind a specific DNA sequence in the promoter of a florigenic rice gene. Mining genetic diversity becomes thus instrumental to define the molecular properties of regulatory pathways.

Elongated Hypocotyl 5-Homolog (HYH) Negatively Regulates Expression of the Ambient Temperature-Responsive MicroRNA Gene MIR169

Arabidopsis microRNA169 (miR169) is an ambient temperature-responsive microRNA that plays an important role in stress responses and the floral transition. However, the transcription factors that regulate the expression of MIR169 have remained unknown. In this study, we show that Elongated Hypocotyl 5-Homolog (HYH) directly binds to the promoter of MIR169a and negatively regulates its expression. Absolute quantification identified MIR169a as the major locus producing miR169. GUS reporter assays revealed that the deletion of a 498-bp fragment (-1,505 to -1,007, relative to the major transcriptional start site) of MIR169a abolished its ambient temperature-responsive expression. DNA-affinity chromatography followed by liquid chromatography-mass spectrometry analysis identified transcription factor HYH as a trans-acting factor that binds to the 498-bp promoter fragment of pri-miR169a. Electrophoretic mobility shift assays and chromatin immunoprecipitation-quantitative PCR demonstrated that the HYH.2 protein, a predominant isoform of HYH, directly associated with a G-box-like motif in the 498-bp fragment of pri-miR169a. Higher enrichment of HYH.2 protein on the promoter region of MIR169a was seen at 23°C, consistent with the presence of more HYH.2 protein in the cell at the temperature. Transcript levels of pri-miR169a increased in hyh mutants and decreased in transgenic plants overexpressing HYH. Consistent with the negative regulation of MIR169a by HYH, the diurnal levels of HYH mRNA and pri-miR169a showed opposite patterns. Taken together, our results suggest that HYH is a transcription factor that binds to a G-box-like motif in the MIR169a promoter and negatively regulates ambient temperature-responsive expression of MIR169a at higher temperatures in Arabidopsis.

NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T

Photoperiod dependent flowering is one of several mechanisms used by plants to initiate the developmental transition from vegetative growth to reproductive growth. The NUCLEAR FACTOR Y (NF-Y) transcription factors are heterotrimeric complexes composed of NF-YA and histone-fold domain (HFD) containing NF-YB/NF-YC, that initiate photoperiod-dependent flowering by cooperatively interacting with CONSTANS (CO) to drive the expression of FLOWERING LOCUS T (FT). This involves NF-Y and CO binding at distal CCAAT and proximal “CORE” elements, respectively, in the FT promoter. While this is well established for the HFD subunits, there remains some question over the potential role of NF-YA as either positive or negative regulators of this process. Here we provide strong support, in the form of genetic and biochemical analyses, that NF-YA, in complex with NF-YB/NF-YC proteins, can directly bind the distal CCAAT box in the FT promoter and are positive regulators of flowering in an FT-dependent manner.

For plants to have reproductive success, they must time their flowering with the most beneficial biotic and abiotic environmental conditions—after all, reproductive success would likely be low if flowers developed when pollinators were not present or freezing temperatures were on the horizon. Proper timing mechanisms for flowering vary significantly between different species, but can be connected to a variety of environmental cues, including water availability, temperature, and day length. Numerous labs have studied the molecular aspects of these timing mechanisms and discovered that many of these pathways converge on the gene FLOWERING LOCUS T (FT). This means that understanding precisely how this gene is regulated can teach us a lot about many plant species in both natural and agricultural settings. In the current study, we focus on day length as an essential cue for flowering in the plant species Arabidopsis thaliana. We further unravel the complexity of FT regulation by clarifying the roles of NUCLEAR FACTOR Y genes in day length perception.

Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress

NF-Ys are heterotrimeric transcription factors composed by the NF-YA, NF-YB and NF-YC subunits. In plants, NF-Y subunits are encoded by multigene families whose members show structural and functional diversifications. An increasing number of NF-Y genes has been shown to play key roles during different stages of root nodule and arbuscular mycorrhizal symbiosis, as well as during the interaction of plants with pathogenic microorganisms. Individual members of the NF-YA and NF-YB families have also been implicated in the development of primary and lateral roots. In addition, different members of the NF-YA and NF-YB gene families from mono- and di-cotyledonous plants have been involved in plant responses to water and nutrient scarcity. This review presents the most relevant and striking results concerning these NF-Y subunits. A phylogenetic analysis of the functionally characterized NF-Y genes revealed that, across plant species, NF-Y proteins functioning in the same biological process tend to belong to common phylogenetic groups. Finally, we discuss the forthcoming challenges of plant NF-Y research, including the detailed dissection of expression patterns, the elucidation of functional specificities as well as the characterization of the potential NF-Y-mediated epigenetic mechanisms by which they control the expression of their target genes. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.

Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family

Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell divisions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.

The multifaceted roles of NUCLEAR FACTOR-Y in Arabidopsis thaliana development and stress responses

NUCLEAR FACTOR-Y (NF-Y) is a heterotrimeric transcription factor (TF) consisting of evolutionarily distinct NF-YA, NF-YB and NF-YC subunits. The functional NF-Y heterotrimer binds to CCAAT elements in eukaryotic gene promoters and influences their expression. The genome of the model organism Arabidopsis thaliana encodes 10 distinct NF-YA, NF-YB, and NF-YC proteins, allowing for enormous combinatorial and functional diversity. Two decades of research have elucidated the importance of NF-Ys in plant growth, development and stress responses; however, the molecular mechanisms of action remain largely unexplored. Intriguingly, recent evidence suggests that NF-Ys are frequently associated with other groups of TFs, expanding the potential NF-Y combinatorial complexity. Further, information regarding the regulation of individual NF-Y subunits at the transcriptional and post-transcriptional level is beginning to emerge. In this review, we will identify developing trends within the NF-Y field and discuss recent progress towards a better understanding of NF-Y function, molecular action, and regulation in the context of Arabidopsis. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.

Y flowering? Regulation and activity of CONSTANS and CCT-domain proteins in Arabidopsis and crop species

Changes in day length regulate the proper timing of flowering in several plant species. The genetic architecture of this process is based on CCT-domain proteins, many of which interact with NF-Y subunits to regulate transcription of target genes. In the model plant Arabidopsis thaliana, the CONSTANS CCT-domain protein is a central photoperiodic sensor. We will discuss how the diurnal rhythms of its transcription and protein accumulation are generated, and how the protein engages into multiple complexes to control production of a systemic flowering signal. Regulatory parallels will be drawn between Arabidopsis and major crops that indicate conservation of some CCT/NF-Y modules during plant evolution. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.

NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana

Recent reports suggest that NF-Y transcription factors are positive regulators of skotomorphogenesis in Arabidopsis thaliana. Three NF-YC genes (NF-YC3, NF-YC4, and NF-YC9) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leucine zipper (bZIP) transcription factors. This included ELONGATED HYPOCOTYL 5 (HY5), which has well-demonstrated roles in photomorphogenesis. Similar to hy5 mutants, we report that nf-yc3 nf-yc4 nf-yc9 triple mutants failed to inhibit hypocotyl elongation in all tested light wavelengths. Surprisingly, nf-yc3 nf-yc4 nf-yc9 hy5 mutants had synergistic defects in light perception, suggesting that NF-Ys represent a parallel light signaling pathway. As with other photomorphogenic transcription factors, nf-yc3 nf-yc4 nf-yc9 triple mutants also partially suppressed the short hypocotyl and dwarf rosette phenotypes of CONSTITUTIVE PHOTOMORPHOGENIC 1 (cop1) mutants. Thus, our data strongly suggest that NF-Y transcription factors have important roles as positive regulators of photomorphogenesis, and in conjunction with other recent reports, implies that the NF-Y are multifaceted regulators of early seedling development.

Light perception is critically important for the fitness of plants in both natural and agricultural settings. Plants not only use light for photosynthesis, but also as a cue for proper development. As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit. When blue and red wavelengths are the dominant sources of light, plants will undergo photomorphogenesis. Photomorphogenesis describes a number of developmental responses initiated by light in a seedling, and includes shortened stems and establishing the ability to photosynthesize. The genes regulating photomorphogenesis have been studied extensively, but a complete picture remains elusive. Here we describe the finding that NUCLEAR FACTOR-Y (NF-Y) genes are positive regulators of photomorphogenesis—i.e., in plants where NF-Y genes are mutated, they display some characteristics of dark grown plants, even though they are in the light. Our data suggests that the roles of NF-Y genes in light perception do not fit in easily with those of other described pathways. Thus, studying these genes promises to help develop a more complete picture of how light drives plant development.

The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis

The antagonistic crosstalk between gibberellic acid (GA) and abscisic acid (ABA) plays a pivotal role in the modulation of seed germination. However, the molecular mechanism of such phytohormone interaction remains largely elusive. Here we show that three Arabidopsis NUCLEAR FACTOR-Y C (NF-YC) homologues NF-YC3, NF-YC4 and NF-YC9 redundantly modulate GA- and ABA-mediated seed germination. These NF-YCs interact with the DELLA protein RGL2, a key repressor of GA signalling. The NF-YC–RGL2 module targets ABI5, a gene encoding a core component of ABA signalling, via specific CCAAT elements and collectively regulates a set of GA- and ABA-responsive genes, thus controlling germination. These results suggest that the NF-YC–RGL2–ABI5 module integrates GA and ABA signalling pathways during seed germination.

Crosstalk between gibberellic acid (GA) and abscisic acid (ABA) regulates seed germination. Here the authors show that NF-YC transcription factors can interact with the RGL2 DELLA protein to regulate expression of ABI5 and therefore modulate ABA- and GA-responsive gene expression.

Genome-wide identification and characterization of the NF-Y gene family in grape (vitis vinifera L.)

Background

Nuclear factor Y (NF-Y) transcription factor is composed of three distinct subunits: NF-YA, NF-YB and NF-YC. Many members of NF-Y family have been reported to be key regulators in plant development, phytohormone signaling and drought tolerance. However, the function of the NF-Y family is less known in grape (Vitis vinifera L.).

Results

A total of 34 grape NF-Y genes that distributed unevenly on grape (V. vinifera) chromosomes were identified in this study. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana and grape NF-Y genes. Comparison of the structures of grape NF-Y genes (VvNF-Ys) revealed their functional conservation and alteration. Furthermore, we investigated the expression profiles of VvNF-Ys in response to various stresses, phytohormone treatments, and in leaves and grape berries with various sugar contents at different developmental stages. The relationship between VvNF-Y transcript levels and sugar content was examined to select candidates for exogenous sugar treatments. Quantitative real-time PCR (qPCR) indicated that many VvNF-Ys responded to different sugar stimuli with variations in transcript abundance. qPCR and publicly available microarray data suggest that VvNF-Ys exhibit distinct expression patterns in different grape organs and developmental stages, and a number of VvNF-Ys may participate in responses to multiple abiotic and biotic stresses, phytohormone treatments and sugar accumulation or metabolism.

Conclusions

In this study, we characterized 34 VvNF-Ys based on their distributions on chromosomes, gene structures, phylogenetic relationship with Arabidopsis NF-Y genes, and their expression patterns. The potential roles of VvNF-Ys in sugar accumulation or metabolism were also investigated. Altogether, the data provide significant insights on VvNF-Ys, and lay foundations for further functional studies of NF-Y genes in grape.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2989-3) contains supplementary material, which is available to authorized users.

Isolation, structural analysis, and expression characteristics of the maize nuclear factor Y gene families

NUCLEAR FACTOR-Y (NF-Y) has been shown to play an important role in growth, development, and response to environmental stress. A NF-Y complex, which consists of three subunits, NF-YA, NF-YB, and, NF-YC, binds to CCAAT sequences in a promoter to control the expression of target genes. Although NF-Y proteins have been reported in Arabidopsis and rice, a comprehensive and systematic analysis of ZmNF-Y genes has not yet been performed. To examine the functions of ZmNF-Y genes in this family, we isolated and characterized 50 ZmNF-Y (14 ZmNF-YA, 18 ZmNF-YB, and 18 ZmNF-YC) genes in an analysis of the maize genome. The 50 ZmNF-Y genes were distributed on all 10 maize chromosomes, and 12 paralogs were identified. Multiple alignments showed that maize ZmNF-Y family proteins had conserved regions and relatively variable N-terminal or C-terminal domains. The comparative syntenic map illustrated 40 paralogous NF-Y gene pairs among the 10 maize chromosomes. Microarray data showed that the ZmNF-Y genes had tissue-specific expression patterns in various maize developmental stages and in response to biotic and abiotic stresses. The results suggested that ZmNF-YB2, 4, 8, 10, 13, and 16 and ZmNF-YC6, 8, and 15 were induced, while ZmNF-YA1, 3, 4, 6, 7, 10, 12, and 13, ZmNF-YB15, and ZmNF-YC3 and 9 were suppressed by drought stress. ZmNF-YA3, ZmNF-YA8 and ZmNF-YA12 were upregulated after infection by the three pathogens, while ZmNF-YA1 and ZmNF-YB2 were suppressed. These results indicate that the ZmNF-Ys may have significant roles in the response to abiotic and biotic stresses.

Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway

Bacterial wilt caused by Ralstonia solanacearum is one of the most destructive bacterial plant diseases. Although many molecular determinants involved in R. solanacearum adaptation to hosts and pathogenesis have been described, host components required for disease establishment remain poorly characterized. Phenotypical analysis of Arabidopsis mutants for leucine-rich repeat (LRR)-receptor-like proteins revealed that mutations in the CLAVATA1 (CLV1) and CLAVATA2 (CLV2) genes confer enhanced disease resistance to bacterial wilt. We further investigated the underlying mechanisms using genetic, transcriptomic and molecular approaches. The enhanced resistance of both clv1 and clv2 mutants to the bacteria did not require the well characterized CLV signalling modules involved in shoot meristem homeostasis, and was conditioned by neither salicylic acid nor ethylene defence-related hormones. Gene expression microarray analysis performed on clv1 and clv2 revealed deregulation of genes encoding nuclear transcription factor Y subunit alpha (NF-YA) transcription factors whose post-transcriptional regulation is known to involve microRNAs from the miR169 family. Both clv mutants showed a defect in miR169 accumulation. Conversely, overexpression of miR169 abrogated the resistance phenotype of clv mutants. We propose that CLV1 and CLV2, two receptors involved in CLV3 perception during plant development, contribute to bacterial wilt through a signalling pathway involving the miR169/NF-YA module.

Identification of microRNAs and their targets in Paulownia fortunei plants free from phytoplasma pathogen after methyl methane sulfonate treatment

MicroRNAs (miRNAs) play major roles in plant responses to various biotic and abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. Paulownia witches' broom (PaWB) disease caused by phytoplasmas reduces Paulownia production worldwide. In this study, we investigated the miRNA-mediated plant response to PaWB phytoplasma by Illumina sequencing and degradome analysis of Paulownia fortunei small RNAs (sRNAs). The sRNA and degradome libraries were constructed from healthy and diseased P. fortunei plants and the plants free from phytoplasma pathogen after 60 mg L(-1) methyl methane sulfonate treatment. A total of 96 P. fortunei-conserved miRNAs and 83 putative novel miRNAs were identified. Among them, 37 miRNAs (17 conserved, 20 novel) were found to be differentially expressed in response to PaWB phytoplasma infection. In addition, 114 target genes for 18 of the conserved miRNA families and 33 target genes for 15 of the novel miRNAs in P. fortunei were detected. The expression patterns of 14 of the PaWB phytoplasma-responsive miRNAs and 12 target genes were determined by quantitative real-time polymerase chain reaction (qPCR) experiments. A functional analysis of the miRNA targets indicated that these targeted genes may regulate transcription, stress response, nitrogen metabolism, and various other activities. Our results will help identify the potential roles of miRNAs involved in protecting P. fortunei from diseases.

OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice

OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response through the modulation of three flowering-time genes ( Ehd1, Hd3a , and RFT1 ) in rice. Plant NUCLEAR FACTOR Y (NF-Y) transcription factors control numerous developmental processes by forming heterotrimeric complexes, but little is known about their roles in flowering in rice. In this study, it is shown that some subunits of OsNF-YB and OsNF-YC interact with each other, and among them, OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response of rice. Protein interaction studies showed that the physical interactions occurred between the three OsNF-YC proteins (OsNF-YC2, OsNF-YC4 and OsNF-YC6) and three OsNF-YB proteins (OsNF-YB8, OsNF-YB10 and OsNF-YB11). Repression and overexpression of the OsNF-YC2 and OsNF-YC4 genes revealed that they act as inhibitors of flowering only under long-day (LD) conditions. Overexpression of OsNF-YC6, however, promoted flowering only under LD conditions, suggesting it could function as a flowering promoter. These phenotypes correlated with the changes in the expression of three rice flowering-time genes [Early heading date 1 (Ehd1), Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1)]. The diurnal and tissue-specific expression patterns of the subsets of OsNF-YB and OsNF-YC genes were similar to those of CCT domain encoding genes such as OsCO3, Heading date 1 (Hd1) and Ghd7. We propose that OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response by interacting directly with OsNF-YB8, OsNF-YB10 or OsNF-YB11 proteins in rice.

Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening

Background

Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses.

Results

In this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm.

Conclusions

In this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2334-2) contains supplementary material, which is available to authorized users.

Genome- wide characterization of Nuclear Factor Y (NF-Y) gene family of sorghum [Sorghum bicolor (L.) Moench]: a bioinformatics approach

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor (TF) complex with preferential binding to CCAAT elements of promoters, regulating gene expression in most of the higher eukaryotes. The availability of plant genome sequences have revealed multiple number of genes coding for the three subunits, namely NF-YA, NF-YB and NF-YC in contrast to single NF-Y gene for each subunit reported in yeast and animals. A total of 33 NF-YTF comprising of 8 NF-YA, 11 NF-YB and 14 NF-YC subunits were accessed from the sorghum genome. The bioinformatic characterization of NF-Y gene family of sorghum for gene structure, chromosome location, protein motif, phylogeny, gene duplication and in-silico expression under abiotic stresses have been attempted in the present study. The identified SbNF-Y genes are distributed on all the 10 chromosomes of sorghum with variability in the frequency and 18 out of 33 SbNF-Ys were found to be intronless. Segmental duplication event was found to be predominant feature based on gene duplication pattern study. Several orthologs and paralogs groups were disclosed through the comprehensive phylogenetic analysis of SbNF-Y proteins along with 36 Arabidopsis and 28 rice NF-Y proteins. In-silico expression analysis under abiotic stresses using rice transcriptome data revealed several of the sorghum NF-Y genes to be associated with salt, drought, cold and heat stresses.

Identification of Novel Components of the Unfolded Protein Response in Arabidopsis

Unfavorable environmental and developmental conditions may cause disturbances in protein folding in the endoplasmic reticulum (ER) that are recognized and counteracted by components of the Unfolded Protein Response (UPR) signaling pathways. The early cellular responses include transcriptional changes to increase the folding and processing capacity of the ER. In this study, we systematically screened a collection of inducible transgenic Arabidopsis plants expressing a library of transcription factors for resistance toward UPR-inducing chemicals. We identified 23 candidate genes that may function as novel regulators of the UPR and of which only three genes (bZIP10, TBF1, and NF-YB3) were previously associated with the UPR. The putative role of identified candidate genes in the UPR signaling is supported by favorable expression patterns in both developmental and stress transcriptional analyses. We demonstrated that WRKY75 is a genuine regulator of the ER-stress cellular responses as its expression was found to be directly responding to ER stress-inducing chemicals. In addition, transgenic Arabidopsis plants expressing WRKY75 showed resistance toward salt stress, connecting abiotic and ER-stress responses.

The Arabidopsis thaliana Nuclear Factor Y Transcription Factors

Nuclear factor Y (NF-Y) is an evolutionarily conserved trimeric transcription factor complex present in nearly all eukaryotes. The heterotrimeric NF-Y complex consists of three subunits, NF-YA, NF-YB, and NF-YC, and binds to the CCAAT box in the promoter regions of its target genes to regulate their expression. Yeast and mammal genomes generally have single genes with multiple splicing isoforms that encode each NF-Y subunit. By contrast, plant genomes generally have multi-gene families encoding each subunit and these genes are differentially expressed in various tissues or stages. Therefore, different subunit combinations can lead to a wide variety of NF-Y complexes in various tissues, stages, and growth conditions, indicating the potentially diverse functions of this complex in plants. Indeed, many recent studies have proved that the NF-Y complex plays multiple essential roles in plant growth, development, and stress responses. In this review, we highlight recent progress on NF-Y in Arabidopsis thaliana, including NF-Y protein structure, heterotrimeric complex formation, and the molecular mechanism by which NF-Y regulates downstream target gene expression. We then focus on its biological functions and underlying molecular mechanisms. Finally, possible directions for future research on NF-Y are also presented.

A Phylogenetically Conserved Group of Nuclear Factor-Y Transcription Factors Interact to Control Nodulation in Legumes

The endosymbiotic association between legumes and soil bacteria called rhizobia leads to the formation of a new root-derived organ called the nodule in which differentiated bacteria convert atmospheric nitrogen into a form that can be assimilated by the host plant. Successful root infection by rhizobia and nodule organogenesis require the activation of symbiotic genes that are controlled by a set of transcription factors (TFs). We recently identified Medicago truncatula nuclear factor-YA1 (MtNF-YA1) and MtNF-YA2 as two M. truncatula TFs playing a central role during key steps of the Sinorhizobium meliloti-M. truncatula symbiotic interaction. NF-YA TFs interact with NF-YB and NF-YC subunits to regulate target genes containing the CCAAT box consensus sequence. In this study, using a yeast two-hybrid screen approach, we identified the NF-YB and NF-YC subunits able to interact with MtNF-YA1 and MtNF-YA2. In yeast (Saccharomyces cerevisiae) and in planta, we further demonstrated by both coimmunoprecipitation and bimolecular fluorescence complementation that these NF-YA, -B, and -C subunits interact and form a stable NF-Y heterotrimeric complex. Reverse genetic and chromatin immunoprecipitation-PCR approaches revealed the importance of these newly identified NF-YB and NF-YC subunits for rhizobial symbiosis and binding to the promoter of MtERN1 (for Ethylene Responsive factor required for Nodulation), a direct target gene of MtNF-YA1 and MtNF-YA2. Finally, we verified that a similar trimer is formed in planta by the common bean (Phaseolus vulgaris) NF-Y subunits, revealing the existence of evolutionary conserved NF-Y protein complexes to control nodulation in leguminous plants. This sheds light on the process whereby an ancient heterotrimeric TF mainly controlling cell division in animals has acquired specialized functions in plants.

The overexpression of an Amaranthus hypochondriacus NF-YC gene modifies growth and confers water deficit stress resistance in Arabidopsis

Nuclear factor-Y (NF-Y), is a plant heterotrimeric transcription factor constituted by NF-YA, NF-YB and NF-YC subunits. The function of many NF-Y subunits, mostly of the A and B type, has been studied in plants, but knowledge regarding the C subunit remains fragmentary. Here, a water stress-induced NF-YC gene from Amaranthus hypochondriacus (AhNF-YC) was further characterized by its overexpression in transgenic Arabidospis thaliana plants. A role in development was inferred from modified growth rates in root, rosettes and inflorescences recorded in AhNF-YC overexpressing Arabidopsis plants, in addition to a delayed onset of flowering. Also, the overexpression of AhNF-YC caused increased seedling sensitivity to abscisic acid (ABA), and influenced the expression of several genes involved in secondary metabolism, development and ABA-related responses. An altered expression of the latter in water stressed and recovered transgenic plants, together with the observed increase in ABA sensitivity, suggested that their increased water stress resistance was partly ABA-dependent. An untargeted metabolomic analysis also revealed an altered metabolite pattern, both in normal and water stress/recovery conditions. These results suggest that AhNF-YC may play an important regulatory role in both development and stress, and represents a candidate gene for the engineering of abiotic stress resistance in commercial crops.

Arabidopsis LEAFY COTYLEDON1 Mediates Postembryonic Development via Interacting with PHYTOCHROME-INTERACTING FACTOR4

Plants undergo postembryonic growth during the developmental transition from germinating seeds to seedlings. Recent studies suggest LEAFY COTYLEDON1 (LEC1), initially identified as a central regulator in embryogenesis and seed maturation in Arabidopsis thaliana, plays a distinct role in postembryonic development. However, the mechanism by which LEC1 regulates nonembryonic development still remains elusive. In this study, we observed etiolation-related phenotypes in early seedlings of lec1 mutants and inducible LEC1 overexpression transgenic lines. Consistent with this, LEC1 promotes the expression of hypocotyl elongation-related genes in a darkness-dependent manner in spite of the comparable LEC1 transcript levels in the light- and dark-grown seedlings. Furthermore, we show that LEC1 interacts with PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a major transcription modulator in postgermination development, to interdependently regulate hypocotyl elongation-related genes via direct binding to G-box element in the dark. Moreover, loss of LEC1 function suppresses the elongated hypocotyl phenotype of PIF-overaccumulating plants; conversely, inducible overexpression of LEC1 does not rescue the short hypocotyl in pif4 mutants. Our findings reveal that LEC1 acts as a coactivator of PIFs in transcriptional regulation during postembryonic growth, providing a possible mechanism by which plants fine-tune morphological development for their survival during the transition from the embryonic phase to seedling establishment.

Cloning and Characterization of 5' Flanking Regulatory Sequences of AhLEC1B Gene from Arachis Hypogaea L

LEAFY COTYLEDON1 (LEC1) is a B subunit of Nuclear Factor Y (NF-YB) transcription factor that mainly accumulates during embryo development. We cloned the 5' flanking regulatory sequence of AhLEC1B gene, a homolog of Arabidopsis LEC1, and analyzed its regulatory elements using online software. To identify the crucial regulatory region, we generated a series of GUS expression frameworks driven by different length promoters with 5' terminal and/or 3' terminal deletion. We further characterized the GUS expression patterns in the transgenic Arabidopsis lines. Our results show that both the 65 bp proximal promoter region and the 52 bp 5' UTR of AhLEC1B contain the key motifs required for the essential promoting activity. Moreover, AhLEC1B is preferentially expressed in the embryo and is co-regulated by binding of its upstream genes with both positive and negative corresponding cis-regulatory elements.

Identification and expression profile analysis of NUCLEAR FACTOR-Y families in Physcomitrella patens

NUCLEAR FACTOR Y transcription factors belong to a multimember family and consist of NF-YA/B/C subunits. Members of the NF-Y family have been reported to regulate physiological processes in plant. In this study, we identified and annotated two NF-YA, nine NF-B, and twelve NF-YC proteins in the genome of Physcomitrella patens. Analyses of conserved domains demonstrated that PpNF-YA/B/C shared the same conserved domains with their orthologous proteins in Arabidopsis, O. sativa and mouse. Expression profiles indicated that PpNF-Ys were widely expressed in different tissues and developmental stages of P. patens throughout protonema and gametophores. The majority of PpNF-Y genes were responsive to abiotic stress via either ABA-independent or -dependent pathways. Some of ABA-regulated PpNF-Y expression were mediated by ABI3. To our knowledge, this study was the first to evaluate NF-Y families in Physcomitrella patens, and provides a foundation to dissect the function of PpNF-Ys.

Discovery of microRNAs and transcript targets related to witches' broom disease in Paulownia fortunei by high-throughput sequencing and degradome approach

Paulownia witches' broom (PaWB) caused by the phytoplasma is a devastating disease of Paulownia trees. It has caused heavy yield losses to Paulownia production worldwide. However, knowledge of the transcriptional and post-transcriptional regulation of gene expression by microRNAs (miRNAs), especially miRNAs responsive to PaWB disease stress, is still rudimentary. In this study, to identify miRNAs and their transcript targets that are responsive to PaWB disease stress, six sequencing libraries were constructed from healthy (PF), PaWB-infected (PFI), and PaWB-infected, 20 mg L(-1) methyl methane sulfonate-treated (PFI20) P. fortunei seedlings. As a result, 95 conserved miRNAs belonging to 18 miRNA families, as well as 122 potential novel miRNAs, were identified. Most of them were found to be a response to PaWB disease-induced stress, and the expression levels of these miRNAs were validated by quantitative real-time PCR analysis. The study simultaneously identified 109 target genes from the P. fortunei for 14 conserved miRNA families and 24 novel miRNAs by degradome sequencing. Furthermore, the functions of the miRNA targets were annotated based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The results presented here provide the groundwork for further analysis of miRNAs and target genes responsive to the PaWB disease stress, and could be also useful for addressing new questions to better understand the mechanisms of plant infection by phytoplasma in the future.

Prunus transcription factors: breeding perspectives

Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs). In peach, 1533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA, and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq) and RNA sequencing (RNA-Seq). New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing) may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci) map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome.