The GCR1, GPA1, PRN1, NF-Y signal chain mediates both blue light and abscisic acid responses in Arabidopsis

Proteome-wide analysis reveals G protein-coupled receptor-like proteins in rice (Oryza sativa)

G protein-coupled receptors (GPCRs) constitute the largest family of transmembrane proteins in metazoans that mediate the regulation of various physiological responses to discrete ligands through heterotrimeric G protein subunits. The existence of GPCRs in plant is contentious, but their comparable crucial role in various signaling pathways necessitates the identification of novel remote GPCR-like proteins that essentially interact with the plant G protein α subunit and facilitate the transduction of various stimuli. In this study, we identified three putative GPCR-like proteins (OsGPCRLPs) (LOC_Os06g09930.1, LOC_Os04g36630.1, and LOC_Os01g54784.1) in the rice proteome using a stringent bioinformatics workflow. The identified OsGPCRLPs exhibited a canonical GPCR 'type I' 7TM topology, patterns, and biologically significant sites for membrane anchorage and desensitization. Cluster-based interactome mapping revealed that the identified proteins interact with the G protein α subunit which is a characteristic feature of GPCRs. Computational results showing the interaction of identified GPCR-like proteins with G protein α subunit and its further validation by the membrane yeast-two-hybrid assay strongly suggest the presence of GPCR-like 7TM proteins in the rice proteome. The absence of a regulator of G protein signaling (RGS) box in the C- terminal domain, and the presence of signature motifs of canonical GPCR in the identified OsGPCRLPs strongly suggest that the rice proteome contains GPCR-like proteins that might be involved in signal transduction.

Cryptococcus neoformans: plant-microbe interactions and ecology

While the opportunistic human pathogens Cryptococcus neoformans and Cryptococcus gattii are often isolated from plants and plant-related material, evidence suggests that these Cryptococcus species do not directly infect plants. Studies find that plants are important for Cryptococcus mating and dispersal. However, these studies have not provided enough detail about how plants and these fungi interact, especially in ways that could show the fungi are capable of causing disease. This review synthesizes recent findings from studies utilizing different plant models associated with the ecology of C. neoformans and C. gattii. Unanswered questions about their environmental role are highlighted. Overall, current research indicates that Cryptococcus utilizes plants as a substrate rather than harming them, arguing against Cryptococcus as a genuine plant pathogen. We hypothesize that plants represent reservoirs that aid dispersal, not hosts vulnerable to infection.

Comprehensive Analyses of Four PhNF-YC Genes from Petunia hybrida and Impacts on Flowering Time

Nuclear Factor Y (NF-Y) is a class of heterotrimeric transcription factors composed of three subunits: NF-A, NF-YB, and NF-YC. NF-YC family members play crucial roles in various developmental processes, particularly in the regulation of flowering time. However, their functions in petunia remain poorly understood. In this study, we isolated four PhNF-YC genes from petunia and confirmed their subcellular localization in both the nucleus and cytoplasm. We analyzed the transcript abundance of all four PhNF-YC genes and found that PhNF-YC2 and PhNF-YC4 were highly expressed in apical buds and leaves, with their transcript levels decreasing before flower bud differentiation. Silencing PhNF-YC2 using VIGS resulted in a delayed flowering time and reduced chlorophyll content, while PhNF-YC4-silenced plants only exhibited a delayed flowering time. Furthermore, we detected the transcript abundance of flowering-related genes involved in different signaling pathways and found that PhCO, PhGI, PhFBP21, PhGA20ox4, and PhSPL9b were regulated by both PhNF-YC2 and PhNF-YC4. Additionally, the transcript abundance of PhSPL2, PhSPL3, and PhSPL4 increased only in PhNF-YC2-silenced plants. Overall, these results provide evidence that PhNF-YC2 and PhNF-YC4 negatively regulate flowering time in petunia by modulating a series of flowering-related genes.

Genome-Wide Identification and Drought Stress Response Pattern of the NF-Y Gene Family in Cymbidium sinense

Cymbidium sinense, a type of orchid plant, is more drought-resistant and ornamental than other terrestrial orchids. Research has shown that many members of the NUCLEAR FACTOR Y (NF-Y) transcription factor family are responsive to plant growth, development, and abiotic stress. However, the mechanism of the NF-Y gene family's response to abiotic stress in orchids has not yet been reported. In this study, phylogenetic analysis allowed for 27 CsNF-Y genes to be identified (5 CsNF-YAs, 9 CsNF-YBs, and 13 CsNF-YC subunits), and the CsNF-Ys were homologous to those in Arabidopsis and Oryza. Protein structure analysis revealed that different subfamilies contained different motifs, but all of them contained Motif 2. Secondary and tertiary protein structure analysis indicated that the CsNF-YB and CsNF-YC subfamilies had a high content of alpha helix structures. Cis-element analysis showed that elements related to drought stress were mainly concentrated in the CsNF-YB and CsNF-YC subfamilies, with CsNF-YB3 and CsNF-YC12 having the highest content. The results of a transcriptome analysis showed that there was a trend of downregulation of almost all CsNF-Ys in leaves under drought stress, while in roots, most members of the CsNF-YB subfamily showed a trend of upregulation. Additionally, seven genes were selected for real-time reverse transcription quantitative PCR (qRT-PCR) experiments. The results were generally consistent with those of the transcriptome analysis. The regulatory roles of CsNF-YB 1, 2, and 4 were particularly evident in the roots. The findings of our study may make a great contribution to the understanding of the role of CsNF-Ys in stress-related metabolic processes.

Moving beyond the arabidopsis-centric view of G-protein signaling in plants

Heterotrimeric G-protein-mediated signaling is a key mechanism to transduce a multitude of endogenous and environmental signals in diverse organisms. The scope and expectations of plant G-protein research were set by pioneering work in metazoans. Given the similarity of the core constituents, G-protein-signaling mechanisms were presumed to be universally conserved. However, because of the enormous diversity of survival strategies and endless forms among eukaryotes, the signal, its interpretation, and responses vary even among different plant groups. Earlier G-protein research in arabidopsis (Arabidopsis thaliana) has emphasized its divergence from Metazoa. Here, we compare recent evidence from diverse plant lineages with the available arabidopsis G-protein model and discuss the conserved and novel protein components, signaling mechanisms, and response regulation.

Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency

KEY MESSAGE

Nitrate-responsive transcriptomic, phenotypic and physiological analyses of rice RGA1 mutant revealed many novel RGA1-regulated genes/processes/traits related to nitrogen use efficiency, and provided robust genetic evidence of RGA1-regulation of NUE. Nitrogen (N) use efficiency (NUE) is important for sustainable agriculture. G-protein signalling was implicated in N-response/NUE in rice, but needed firm genetic characterization of the role of alpha subunit (RGA1). The knock-out mutant of RGA1 in japonica rice exhibited lesser nitrate-dose sensitivity than the wild type (WT), in yield and NUE. We, therefore, investigated its genomewide nitrate-response relative to WT. It revealed 3416 differentially expressed genes (DEGs), including 719 associated with development, grain yield and phenotypic traits for NUE. The upregulated DEGs were related to photosynthesis, chlorophyll, tetrapyrrole and porphyrin biosynthesis, while the downregulated DEGs belonged to cellular protein metabolism and transport, small GTPase signalling, cell redox homeostasis, etc. We validated 26 nitrate-responsive DEGs across functional categories by RT-qPCR. Physiological validation of nitrate-response in the mutant and the WT at 1.5 and 15 mM doses revealed higher chlorophyll and stomatal length but decreased stomatal density, conductance and transpiration. The consequent increase in photosynthesis and water use efficiency may have contributed to better yield and NUE in the mutant, whereas the WT was N-dose sensitive. The mutant was not as N-dose-responsive as the WT in shoot/root growth, productive tillers and heading date, but equally responsive as WT in total N and protein content. The RGA1 mutant was less impacted by higher N-dose or salt stress in terms of yield, protein content, photosynthetic performance, relative water content, water use efficiency and catalase activity. PPI network analyses revealed known NUE-related proteins as RGA1 interactors. Therefore, RGA1 negatively regulates N-dose sensitivity and NUE in rice.

RsGLK2.1-RsNF-YA9a module positively regulates the chlorophyll biosynthesis by activating RsHEMA2 in green taproot of radish

Radish (Raphanus sativus L.) is an economically important and widely cultivated root vegetable crop. The coloration of the green skin and green flesh is an important trait influencing the nutrition and flavor quality in fruit radish. GOLDEN2-LIKEs (GLKs) play critically important roles in plastid development and chlorophyll biosynthesis in plants. However, the molecular mechanism underlying chlorophyll biosynthesis still remain elusive in green fruit radish taproot. Herein, the RsGLK2.1 gene exhibited higher expression level in taproot with a green skin (GS) and green flesh (GF) than that in taproot of the white or red radish genotypes. RsGLK2.1 is a nuclear transcription factor that has intrinsic transcriptional activation activity. Overexpression of RsGLK2.1 increased the total chlorophyll content of 20.68%-45.84% in radish leaves. Knockout of the RsGLK2.1 gene via CRISPR/Cas9 technology resulted in a significant decrease in the chlorophyll content. Overexpression of the RsGLK2.1 gene could restore the phenotype of the glk1glk2 mutant Arabidopsis. RsGLK2.1 was participated in regulating the chlorophyll biosynthesis by directly binding to the promoter of RsHEMA2 and activating its transcription. The interaction of RsNF-YA9a with RsGLK2.1 increased the transcriptional activity of the downstream gene RsHEMA2 under the light condition rather than the dark condition, indicating that both of them regulate the chlorophyll biosynthesis in a light-dependent manner of radish. Overall, these results provided insights into the molecular framework of the RsGLK2.1-RsNF-YA9a module, and could facilitate dissecting the regulatory mechanism underlying chlorophyll biosynthesis in green taproot of radish, and genetic improvement of quality traits in fruit radish breeding programs.

Genome-Wide Identification, Characterization and Expression Analysis of Plant Nuclear Factor (NF-Y) Gene Family Transcription Factors in Saccharum spp

Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of systematic research on the NF-Y gene subfamily in sugarcane. In this study, 51 NF-Y genes (ShNF-Y), composed of 9 NF-YA, 18 NF-YB, and 24 NF-YC genes, were identified in sugarcane (Saccharum spp.). Chromosomal distribution analysis of ShNF-Ys in a Saccharum hybrid located the NF-Y genes on all 10 chromosomes. Multiple sequence alignment (MSA) of ShNF-Y proteins revealed conservation of core functional domains. Sixteen orthologous gene pairs were identified between sugarcane and sorghum. Phylogenetic analysis of NF-Y subunits of sugarcane, sorghum, and Arabidopsis showed that ShNF-YA subunits were equidistant while ShNF-YB and ShNF-YC subunits clustered distinctly, forming closely related and divergent groups. Expression profiling under drought treatment showed that NF-Y gene members were involved in drought tolerance in a Saccharum hybrid and its drought-tolerant wild relative, Erianthus arundinaceus. ShNF-YA5 and ShNF-YB2 genes had significantly higher expression in the root and leaf tissues of both plant species. Similarly, ShNF-YC9 had elevated expression in the leaf and root of E. arundinaceus and in the leaf of a Saccharum hybrid. These results provide valuable genetic resources for further sugarcane crop improvement programs.

Genome-wide identification of NF-Y gene family in maize (Zea mays L.) and the positive role of ZmNF-YC12 in drought resistance and recovery ability

Nuclear factor Y (NF-Y) genes play important roles in many biological processes, such as leaf growth, nitrogen nutrition, and drought resistance. However, the biological functions of these transcription factor family members have not been systematically analyzed in maize. In the present study, a total of 52 ZmNF-Y genes were identified and classified into three groups in the maize genome. An analysis of the evolutionary relationship, gene structure, and conserved motifs of these genes supports the evolutionary conservation of NF-Y family genes in maize. The tissue expression profiles based on RNA-seq data showed that all genes apart from ZmNF-Y16, ZmNF-YC15, and ZmNF-YC17 were expressed in different maize tissues. A weighted correlation network analysis was conducted and a gene co expression network method was used to analyze the transcriptome sequencing results; six core genes responding to drought and rewatering were identified. A real time fluorescence quantitative analysis showed that these six genes responded to high temperature, drought, high salt, and abscisic acid (ABA) treatments, and subsequent restoration to normal levels. ZmNF-YC12 was highly induced by drought and rewatering treatments. The ZmNF-YC12 protein was localized in the nucleus, and the Gal4-LexA/UAS system and a transactivation analysis demonstrated that ZmNF-YC12 in maize (Zea mays L.) is a transcriptional activator that regulates drought resistance and recovery ability. Silencing ZmNF-YC12 reduced net photosynthesis, chlorophyll content, antioxidant (superoxide dismutase, catalase, peroxidase and ascorbate peroxidase) system activation, and soluble protein and proline contents; it increased the malondialdehyde content, the relative water content, and the water loss rate, which weakened drought resistance and the recoverability of maize. These results provide insights into understanding the evolution of ZmNF-Y family genes in maize and their potential roles in genetic improvement. Our work provides a foundation for subsequent functional studies of the NF-Y gene family and provides deep insights into the role of the ZmNF-YC12 regulatory network in controlling drought resistance and the recoverability of maize.

Predicted Three-Dimensional Structure of the GCR1 Putative GPCR in Arabidopsis thaliana and Its Binding to Abscisic Acid and Gibberellin A1

GCR1 has been proposed as a plant analogue to animal G-protein-coupled receptors that can promote or regulate several physiological processes by binding different phytohormones. For instance, abscisic acid (ABA) and gibberellin A1 (GA1) have been shown to promote or regulate germination and flowering, root elongation, dormancy, and biotic and abiotic stresses, among others. They may act through binding to GCR1, which would put GCR1 at the heart of key signaling processes of agronomic importance. Unfortunately, this GPCR function has yet to be fully validated due to the lack of an X-ray or cryo-EM 3D atomistic structure for GCR1. Here, we used the primary sequence data from Arabidopsis thaliana and the GEnSeMBLE complete sampling method to examine 13 trillion possible packings of the 7 transmembrane helical domains corresponding to GCR1 to downselect an ensemble of 25 configurations likely to be accessible to the binding of ABA or GA1. We then predicted the best binding sites and energies for both phytohormones to the best GCR1 configurations. To provide the basis for the experimental validation of our predicted ligand-GCR1 structures, we identify several mutations that should improve or weaken the interactions. Such validations could help establish the physiological role of GCR1 in plants.

Life, death and resurrection of plant GPCRs

The activation of G-protein coupled receptors (GPCRs) by extracellular ligands constitutes the first step of heterotrimeric G-protein signalling in animals. In plants, canonical GPCRs have been known for over 25 years, often in association with agronomically important functions. But their role in plant G-protein signalling and even their annotation as GPCR was contested in the last decade, only to be revisited in the light of more recent evidences. In this first ever review on plant GPCRs, we catalogue all the plant GPCRs described to date and discuss the evidences for and against their role in plants in general and G-protein signalling in particular. We argue against writing off GPCRs and point to the missing links to be investigated to establish firm conclusions either way.

Identification and expression analysis of maize NF-YA subunit genes

NF-YAs encode subunits of the nuclear factor-Y (NF-Y) gene family. NF-YAs represent a kind of conservative transcription factor in plants and are involved in plant growth and development, as well as resistance to biotic and abiotic stress. In this study, 16 maize (Zea mays) NF-YA subunit genes were identified using bioinformatics methods, and they were divided into three categories by a phylogenetic analysis. A conserved domain analysis showed that most contained a CCAAT-binding transcription factor (CBFB) _NF-YA domain. Maize NF-YA subunit genes showed very obvious tissue expression characteristics. The expression level of the NF-YA subunit genes significantly changed under different abiotic stresses, including Fusarium graminearum infection and salicylic acid (SA) or jasmonic acid (JA) treatments. After inoculation with Setosphaeria turcica and Cochliobolus heterostrophus, the lesion areas of nfya01 and nfya06 were significantly larger than that of B73, indicating that ZmNFYA01 and ZmNFYA06 positively regulated maize disease resistance. ZmNFYA01 and ZmNFYA06 may regulated maize disease resistance by affecting the transcription levels of ZmPRs. Thus, NF-YA subunit genes played important roles in promoting maize growth and development and resistance to stress. The results laid a foundation for clarifying the functions and regulatory mechanisms of NF-YA subunit genes in maize.

Ectopic expression of GmNF-YA8 in Arabidopsis delays flowering via modulating the expression of gibberellic acid biosynthesis- and flowering-related genes and promotes lateral root emergence in low phosphorus conditions

NUCLEAR FACTOR Y subunit alpha (NF-YA), together with NF-YB and NF-YC, regulates plant growth and development, as well as plant responses to biotic and abiotic stresses. Although extensive studies have examined the functions of NF-YAs in Arabidopsis thaliana, the roles of NF- YAs in Glycinme max are poorly understood. In this study, we identified a phosphorus (P) starvation-responsive NF-YA8 in soybean. The expression of GmNF-YA8 is induced by low P or low nitrogen in leaves, but not by potassium or iron starvation, respectively. GmNF-YA8 is localized in the nucleus and plasma membrane. Ectopic expression of GmNF-YA8 inhibits plant growth and delayed flowering in Arabidopsis. Exogenous application of gibberellic acid (GA) rescues the delayed flowering phenotype in Arabidopsis overexpressing GmNF-YA8 lines GmNF-YA8OE-05 and GmNF-YA8OE-20. Moreover, quantitative real time PCR (qRT-PCR) verified that overexpression of GmNF-YA8 downregulates GA20ox2 and GA3ox2 expression, but upregulates GA2ox2 and GA2ox3 that encode enzymes, which inactive bioactive GAs. Consistent with the late flowering phenotype of Arabidopsis trangenic lines that overexpress GmNF-YA8, the transcript levels of flowering-promoting genes AP1, CO, LFY, and SOC1 are reduced. In addition, overexpression of GmNF-YA8 promotes the emergence of lateral root (LR) primordium from epidermis rather than the initiation of LR in low P, and increases the LR density in low nitrogen. Our results provide insights into the roles of GmNF-YA8.

A conserved HSF:miR169:NF-YA loop involved in tomato and Arabidopsis heat stress tolerance

Heat stress transcription factors (HSFs) and microRNAs (miRNAs) regulate different stress and developmental networks in plants. Regulatory feedback mechanisms are at the basis of these networks. Here, we report that plants improve their heat stress tolerance through HSF-mediated transcriptional regulation of MIR169 and post-transcriptional regulation of Nuclear Factor-YA (NF-YA) transcription factors. We show that HSFs recognize tomato (Solanum lycopersicum) and Arabidopsis MIR169 promoters using yeast one-hybrid/chromatin immunoprecipitation-quantitative PCR. Silencing tomato HSFs using virus-induced gene silencing (VIGS) reduced Sly-MIR169 levels and enhanced Sly-NF-YA9/A10 target expression. Further, Sly-NF-YA9/A10 VIGS knockdown tomato plants and Arabidopsis plants overexpressing At-MIR169d or At-nf-ya2 mutants showed a link with increased heat tolerance. In contrast, Arabidopsis plants overexpressing At-NF-YA2 and those expressing a non-cleavable At-NF-YA2 form (miR169d-resistant At-NF-YA2) as well as plants in which At-miR169d regulation is inhibited (miR169d mimic plants) were more sensitive to heat stress, highlighting NF-YA as a negative regulator of heat tolerance. Furthermore, post-transcriptional cleavage of NF-YA by elevated miR169 levels resulted in alleviation of the repression of the heat stress effector HSFA7 in tomato and Arabidopsis, revealing a retroactive control of HSFs by the miR169:NF-YA node. Hence, a regulatory feedback loop involving HSFs, miR169s and NF-YAs plays a critical role in the regulation of the heat stress response in tomato and Arabidopsis plants.

Identification and Characterization of Abiotic Stress–Responsive NF-YB Family Genes in Medicago

Nuclear factor YB (NF-YB) are plant-specific transcription factors that play a critical regulatory role in plant growth and development as well as in plant resistance against various stresses. In this study, a total of 49 NF-YB genes were identified from the genomes of Medicago truncatula and Medicago sativa. Multiple sequence alignment analysis showed that all of these NF-YB members contain DNA binding domain, NF-YA interaction domain and NF-YC interaction domain. Phylogenetic analysis suggested that these NF-YB proteins could be classified into five distinct clusters. We also analyzed the exon–intron organizations and conserved motifs of these NF-YB genes and their deduced proteins. We also found many stress-related cis-acting elements in their promoter region. In addition, analyses on genechip for M. truncatula and transcriptome data for M. sativa indicated that these NF-YB genes exhibited a distinct expression pattern in various tissues; many of these could be induced by drought and/or salt treatments. In particular, RT-qPCR analysis revealed that the expression levels of gene pairs MsNF-YB27/MtNF-YB15 and MsNF-YB28/MtNF-YB16 were significantly up-regulated under NaCl and mannitol treatments, indicating that they are most likely involved in salt and drought stress response. Taken together, our study on NF-YB family genes in Medicago is valuable for their functional characterization, as well as for the application of NF-YB genes in genetic breeding for high-yield and high-resistance alfalfa.

Rice LEAFY COTYLEDON1 Hinders Embryo Greening During the Seed Development

LEAFY COTYLEDON1 (LEC1) is the central regulator of seed development in Arabidopsis, while its function in monocots is largely elusive. We generated Oslec1 mutants using CRISPR/Cas9 technology. Oslec1 mutant seeds lost desiccation tolerance and triggered embryo greening at the early development stage. Transcriptome analysis demonstrated that Oslec1 mutation altered diverse hormonal pathways and stress response in seed maturation, and promoted a series of photosynthesis-related genes. Further, genome-wide identification of OsLEC1-binding sites demonstrated that OsLEC1 bound to genes involved in photosynthesis, photomorphogenesis, as well as abscisic acid (ABA) and gibberellin (GA) pathways, involved in seed maturation. We illustrated an OsLEC1-regulating gene network during seed development, including the interconnection between photosynthesis and ABA/GA biosynthesis/signaling. Our findings suggested that OsLEC1 acts as not only a central regulator of seed maturation but also an inhibitor of embryo greening during rice seed development. This study would provide new understanding for the OsLEC1 regulatory mechanisms on photosynthesis in the monocot seed development.

Genome-wide characterization of nuclear factor Y transcription factors in Fagopyrum tataricum

The nuclear factor Y (NF-Y) is an important transcription factor family that regulates plant developmental processes and abiotic stress responses. Currently, genome-wide studies of the NF-Y family are limited in Fagopyrum tataricum, an important economic crop. Based on the released genome assembly, we predicted a total of 38 NF-Y encoding genes (FtNF-Ys), including 12 FtNF-YAs, 18 FtNF-YBs, and eight FtNF-YCs subunits, in F. tataricum. Phylogenetic tree and sequence alignments showed that FtNF-Ys were conserved between F. tataricum and other species. Tissue expressions and network analyses suggested that FtNF-Ys might be involved in regulating developmental processes in different tissues. Several FtNF-YAs and FtNF-Ybs were also potentially involved in light response. In addition, FtNF-YC-like1 and FtNF-YC-like2 partially rescued the late flowering phenotype in nf-yc1 nf-yc3 nf-yc4 nf-yc9 (ycQ) mutant in Arabidopsis thaliana, supporting a conserved role of FtNF-Ys in regulating developmental processes. Together, the genomic information provides a comprehensive understanding of the NF-Y transcription factors in F. tataricum, which will be useful for further investigation of their functions in F. tataricum.

Genetic architecture of variation in Arabidopsis thaliana rosettes

Rosette morphology across Arabidopsis accessions exhibits considerable variation. Here we report a high-throughput phenotyping approach based on automatic image analysis to quantify rosette shape and dissect the underlying genetic architecture. Shape measurements of the rosettes in a core set of Recombinant Inbred Lines from an advanced mapping population (Multiparent Advanced Generation Inter-Cross or MAGIC) derived from inter-crossing 19 natural accessions. Image acquisition and analysis was scaled to extract geometric descriptors from time stamped images of growing rosettes. Shape analyses revealed heritable morphological variation at early juvenile stages and QTL mapping resulted in over 116 chromosomal regions associated with trait variation within the population. Many QTL linked to variation in shape were located near genes related to hormonal signalling and signal transduction pathways while others are involved in shade avoidance and transition to flowering. Our results suggest rosette shape arises from modular integration of sub-organ morphologies and can be considered a functional trait subjected to selective pressures of subsequent morphological traits. On an applied aspect, QTLs found will be candidates for further research on plant architecture.

PpSnRK1α overexpression alters the response to light and affects photosynthesis and carbon metabolism in tomato

Sucrose nonfermentation 1 (SNF1) related kinase 1 (SnRK1) is a central energy sensor kinase in plants and a key switch regulating carbon and nitrogen metabolism. Fruit quality depends on leaf photosynthetic efficiency and carbohydrate accumulation, but the role of peach (Prunus persica) SnRK1 α subunit (PpSnRK1α) in regulating leaf carbon metabolism and the light signal response remains unclear. We studied the carbon metabolism of tomato leaves overexpressing PpSnRK1α and the responses of PpSnRK1α-overexpressing tomato leaves to light signals. Transcriptome, metabolome, and real-time quantitative polymerase chain reaction analyses revealed that uridine 5'-diphosphoglucose, glutamate, and glucose-6-phosphate accumulated in tomato leaves overexpressing PpSnRK1α. The expression of genes (e.g., GDH2, SuSy) encoding enzymes related to carbon metabolism (e.g., glutamate dehydrogenase (GDH2; EC: 1.4.1.3), sucrose synthase (SS; EC: 2.4.1.13)) and chlorophyllase (CLH) encoding chlorophyllase (EC: 3.1.1.14), which regulates photosynthetic pigments and photosynthesis, was significantly increased in PpSnRK1α-overexpressing plants. PpSnRK1α overexpression inhibited the growth of hypocotyls and primary roots in response to light. The chlorophyll content of the leaves was increased, the activity of SS and ADPG pyrophosphatase (AGPase; EC: 2.7.7.27) was increased, and photosynthesis was promoted in PpSnRK1α-overexpressing plants relative to wild-type plants. Under light stress, the net photosynthetic rate of plants was significantly higher in plants overexpressing PpSnRK1α than in wild-type plants. This indicates that PpSnRK1α promotes the accumulation of carbohydrates by regulating genes related to carbon metabolism, regulating genes related to chlorophyll synthesis, and then responding to light signals to increase the net photosynthetic rate of leaves.

Modulation of NF-YB genes in Ricinus communis L. in response to different temperatures and developmental stages and functional characterization of RcNF-YB8 as an important regulator of flowering time in Arabidopsis thaliana

We have characterized the NF-YB gene family in R. communis using bioinformatics, ecotopic expression, and transcriptomics. A total of 14 RcNF-YB genes were identified in R. communis genome using the conserved NF-YB region. This number is similar to what is found in A. thaliana (13 genes) and O. sativa (11 genes), whereas it is considerably lower to what is found in P. trichocarpa (21 genes) and S. lycopersycum (29 genes). Several regulatory cis-elements were identified in the promoter region, including low temperature, defense and stress, MIC, MYB, and abscisic acid. RcNF-YB is strongly modulated by temperature and it is dependent on the stage of germination. In general, RcNF-YB genes showed higher expression levels in dry seeds and early imbibition (EI) samples as compared to later stages of seedling development. Ectopic expression of RcNF-YB8 reduced flowering time in Arabidopsis reducing the time required for the formation of the first visible bud, the time required to open the first flower, and the time required for the formation of the first visible silique. At the end of the life cycle, ectopic expression of RcNF-YB8 affected plant height (PH), silique length (SL), the total number of silique per plant, 1000-seed weight, and seed size. Our data demonstrated the role of RcNF-YB8 in flowering time, plant height and seed production, and it shows that it may constitute a key target gene for breeding superior R. communis genotypes.

Cloning and functional characterization of seed-specific LEC1A promoter from peanut (Arachis hypogaea L.)

LEAFY COTYLEDON1 (LEC1) is a HAP3 subunit of CCAAT-binding transcription factor, which controls several aspects of embryo and postembryo development, including embryo morphogenesis, storage reserve accumulation and skotomorphogenesis. Herein, using the method of chromosomal walking, a 2707bp upstream sequence from the ATG initiation codon site of AhLEC1A which is a homolog of Arabidopsis LEC1 was isolated in peanut. Its transcriptional start site confirmed by 5’ RACE was located at 82 nt from 5’ upstream of ATG. The bioinformatics analysis revealed that there existed many tissue-specific elements and light responsive motifs in its promoter. To identify the functional region of the AhLEC1A promoter, seven plant expression vectors expressing the GUS (β-glucuronidase) gene, driven by 5’ terminal series deleted fragments of AhLEC1A promoter, were constructed and transformed into Arabidopsis. Results of GUS histochemical staining showed that the regulatory region containing 82bp of 5’ UTR and 2228bp promoter could facilitate GUS to express preferentially in the embryos at different development periods of Arabidopsis. Taken together, it was inferred that the expression of AhLEC1A during seed development of peanut might be controlled positively by several seed-specific regulatory elements, as well as negatively by some other regulatory elements inhibiting its expression in other organs. Moreover, the GUS expression pattern of transgenic seedlings in darkness and in light was relevant to the light-responsive elements scattered in AhLEC1A promoter segment, implying that these light-responsive elements harbored in the AhLEC1A promoter regulate skotomorphogenesis of peanut seeds, and AhLEC1A expression was inhibited after the germinated seedlings were transferred from darkness to light.

Heterotrimeric G-protein α subunit (RGA1) regulates tiller development, yield, cell wall, nitrogen response and biotic stress in rice

G-proteins are implicated in plant productivity, but their genome-wide roles in regulating agronomically important traits remain uncharacterized. Transcriptomic analyses of rice G-protein alpha subunit mutant (rga1) revealed 2270 differentially expressed genes (DEGs) including those involved in C/N and lipid metabolism, cell wall, hormones and stress. Many DEGs were associated with root, leaf, culm, inflorescence, panicle, grain yield and heading date. The mutant performed better in total weight of filled grains, ratio of filled to unfilled grains and tillers per plant. Protein–protein interaction (PPI) network analysis using experimentally validated interactors revealed many RGA1-responsive genes involved in tiller development. qPCR validated the differential expression of genes involved in strigolactone-mediated tiller formation and grain development. Further, the mutant growth and biomass were unaffected by submergence indicating its role in submergence response. Transcription factor network analysis revealed the importance of RGA1 in nitrogen signaling with DEGs such as Nin-like, WRKY, NAC, bHLH families, nitrite reductase, glutamine synthetase, OsCIPK23 and urea transporter. Sub-clustering of DEGs-associated PPI network revealed that RGA1 regulates metabolism, stress and gene regulation among others. Predicted rice G-protein networks mapped DEGs and revealed potential effectors. Thus, this study expands the roles of RGA1 to agronomically important traits and reveals their underlying processes.

Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica)

The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.

Genome-wide identification of NF-YA gene family in cotton and the positive role of GhNF-YA10 and GhNF-YA23 in salt tolerance

Nuclear factor YA (NF-YA) genes play important roles in many biological processes, such as leaf growth, nitrogen nutrition, drought resistance, and salt stress. The functions of NF-YA genes in cotton have not been elucidated. The current study identified a total of 16, 16, 31, and 29 genes from Gossypium raimondii, G. arboretum, G. barbadense, and G. hirsutum, respectively. The NF-YA genes in cotton were phylogenetically classified into 4 groups. Analysis of gene structure, conserved motifs and multiple sequence alignments supported the evolutionary conservation of NF-YA family genes in cotton. Analysis of the expression patterns of GhNF-YAs in cotton suggested that GhNF-YAs play important roles in plant growth, development, and stress responses. The quantitative real-time PCR (qRT-PCR) validation of selected genes suggested that GhNF-YA genes are induced in response to salt, drought, ABA, and MeJA treatments. GhNF-YA genes may regulate salt and drought stress via the ABA or MeJA pathway. Silencing of GhNF-YA10 and GhNF-YA23 significantly reduced the salt tolerance of cotton seedlings, indicating that these genes participate in the regulation of the response of cotton to salt stress. These results establish a foundation for subsequent functional studies of the NF-YA gene family in cotton.

Heterotrimeric G-Protein Interactions Are Conserved Despite Regulatory Element Loss in Some Plants

Heterotrimeric G-proteins are key modulators of multiple signaling and development pathways in plants and regulate many agronomic traits, including architecture and grain yield. Regulator of G-protein signaling (RGS) proteins are an integral part of the G-protein networks; however, these are lost in many monocots. To assess if the loss of RGS in specific plants has resulted in altered G-protein networks and the extent to which RGS function is conserved across contrasting monocots, we explored G-protein-dependent developmental pathways in Brachypodium distachyon and Setaria viridis, representing species without or with a native RGS, respectively. Artificial microRNA-based suppression of Gα in both species resulted in similar phenotypes. Moreover, overexpression of Setaria italica RGS in B. distachyon resulted in phenotypes similar to the suppression of BdGα This effect of RGS overexpression depended on its ability to deactivate Gα, as overexpression of a biochemically inactive variant protein resulted in plants indistinguishable from the wild type. Comparative transcriptome analysis of B. distachyon plants with suppressed levels of Gα or overexpression of RGS showed significant overlap of differentially regulated genes, corroborating the phenotypic data. These results suggest that despite the loss of RGS in many monocots, the G-protein functional networks are maintained, and Gα proteins have retained their ability to be deactivated by RGS.

Heterotrimeric G-proteins mediated hormonal responses in plants

Phytohormones not only orchestrate intrinsic developmental programs from germination to senescence but also regulate environmental inputs through complex signalling pathways. Despite building an own signalling network, hormones mutually contribute several signalling systems, which are also essential for plant growth and development, defense, and responses to abiotic stresses. One of such important signalling cascades is G-proteins, which act as critical regulators of a wide range of fundamental cellular processes by transducing receptor signals to the intracellular environment. G proteins are composed of α, β, and γ subunits, and the molecular switching between active and inactive conformation of Gα controls the signalling cycle. The active GTP bound Gα and freed Gβγ have both independent and tightly coordinated roles in the regulation of effector molecules, thereby modulating multiple responses, including hormonal responses. Therefore, an interplay of hormones with G-proteins fine-tunes multiple biological processes of plants; however, their molecular mechanisms are largely unknown. Functional characterization of hormone biosynthesis, perception, and signalling components, as well as identification of few effector molecules of G-proteins and their interaction networks, reduces the complexity of the hormonal signalling networks related to G-proteins. In this review, we highlight a valuable insight into the mechanisms of how the G-protein signalling cascades connect with hormonal responses to regulate increased developmental flexibility as well as remarkable plasticity of plants.

Sequence analysis and protein interactions of Arabidopsis CIA2 and CIL proteins

BACKGROUND

A previous screening of Arabidopsis thaliana for mutants exhibiting dysfunctional chloroplast protein transport identified the chloroplast import apparatus (cia) gene. The cia2 mutant has a pale green phenotype and reduced rate of protein import into chloroplasts, but leaf shape and size are similar to wild-type plants of the same developmental stage. Microarray analysis showed that nuclear CIA2 protein enhances expression of the Toc75, Toc33, CPN10 and cpRPs genes, thereby up-regulating protein import and synthesis efficiency in chloroplasts. CIA2-like (CIL) shares 65% sequence identity to CIA2, suggesting that CIL and CIA2 are homologous proteins in Arabidopsis. Here, we further assess the protein interactions and sequence features of CIA2 and CIL.

RESULTS

Subcellular localizations of truncated CIA2 protein fragments in our onion transient assay demonstrate that CIA2 contains two nuclear localization signals (NLS) located at amino acids (aa) 62-65 and 291-308, whereas CIL has only one NLS at aa 47-50. We screened a yeast two-hybrid (Y2H) Arabidopsis cDNA library to search for putative CIA2-interacting proteins and identified 12 nuclear proteins, including itself, CIL, and flowering-control proteins (such as CO, NF-YB1, NF-YC1, NF-YC9 and ABI3). Additional Y2H experiments demonstrate that CIA2 and CIL mainly interact with flowering-control proteins via their N-termini, but preferentially form homo- or hetero-dimers through their C-termini. Moreover, sequence alignment showed that the N-terminal sequences of CIA2, CIL and NF-YA are highly conserved. Therefore, NF-YA in the NF-Y complex could be substituted by CIA2 or CIL.

CONCLUSIONS

We show that Arabidopsis CIA2 and CIL can interact with CO and NF-Y complex, so not only may they contribute to regulate chloroplast function but also to modulate flower development.

Envisioning the immune interactome in Arabidopsis

During plant-pathogen interaction, immune targets were regulated by protein-protein interaction events such as ligand-receptor/co-receptor, kinase-substrate, protein sequestration, activation or repression via post-translational modification and homo/oligo/hetro-dimerisation of proteins. A judicious use of molecular machinery requires coordinated protein interaction among defence components. Immune signalling in Arabidopsis can be broadly represented in successive or simultaneous steps; pathogen recognition at cell surface, Ca2+ and reactive oxygen species signalling, MAPK signalling, post-translational modification, transcriptional regulation and phyto-hormone signalling. Proteome wide interaction studies have shown the existence of interaction hubs associated with physiological function. So far, a number of protein interaction events regulating immune targets have been identified, but their understanding in an interactome view is lacking. We focussed specifically on the integration of protein interaction signalling in context to plant-pathogenesis and identified the key targets. The present review focuses towards a comprehensive view of the plant immune interactome including signal perception, progression, integration and physiological response during plant pathogen interaction.

Translational regulation contributes to the elevated CO2 response in two Solanum species

Understanding the impact of elevated CO2 (eCO2 ) in global agriculture is important given climate change projections. Breeding climate-resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2 , from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2 .

Flexible functional interactions between G-protein subunits contribute to the specificity of plant responses

Plants being sessile integrate information from a variety of endogenous and external cues simultaneously to optimize growth and development. This necessitates the signaling networks in plants to be highly dynamic and flexible. One such network involves heterotrimeric G-proteins comprised of Gα, Gβ, and Gγ subunits, which influence many aspects of growth, development, and stress response pathways. In plants such as Arabidopsis, a relatively simple repertoire of G-proteins comprised of one canonical and three extra-large Gα, one Gβ and three Gγ subunits exists. Because the Gβ and Gγ proteins form obligate dimers, the phenotypes of plants lacking the sole Gβ or all Gγ genes are similar, as expected. However, Gα proteins can exist either as monomers or in a complex with Gβγ, and the details of combinatorial genetic and physiological interactions of different Gα proteins with the sole Gβ remain unexplored. To evaluate such flexible, signal-dependent interactions and their contribution toward eliciting a specific response, we have generated Arabidopsis mutants lacking specific combinations of Gα and Gβ genes, performed extensive phenotypic analysis, and evaluated the results in the context of subunit usage and interaction specificity. Our data show that multiple mechanistic modes, and in some cases complex epistatic relationships, exist depending on the signal-dependent interactions between the Gα and Gβ proteins. This suggests that, despite their limited numbers, the inherent flexibility of plant G-protein networks provides for the adaptability needed to survive under continuously changing environments.

PIRIN2 suppresses S-type lignin accumulation in a noncell-autonomous manner in Arabidopsis xylem elements

PIRIN (PRN) genes encode cupin domain-containing proteins that function as transcriptional co-regulators in humans but that are poorly described in plants. A previous study in xylogenic cell cultures of Zinnia elegans suggested a role for a PRN protein in lignification. This study aimed to identify the function of Arabidopsis (Arabidopsis thaliana) PRN proteins in lignification of xylem tissues. Chemical composition of the secondary cell walls was analysed in Arabidopsis stems and/or hypocotyls by pyrolysis-gas chromatography/mass spectrometry, 2D-nuclear magnetic resonance and phenolic profiling. Secondary cell walls of individual xylem elements were chemotyped by Fourier transform infrared and Raman microspectroscopy. Arabidopsis PRN2 suppressed accumulation of S-type lignin in Arabidopsis stems and hypocotyls. PRN2 promoter activity and PRN2:GFP fusion protein were localised specifically in cells next to the vessel elements, suggesting a role for PRN2 in noncell-autonomous lignification of xylem vessels. Accordingly, PRN2 modulated lignin chemistry in the secondary cell walls of the neighbouring vessel elements. These results indicate that PRN2 suppresses S-type lignin accumulation in the neighbourhood of xylem vessels to bestow G-type enriched lignin composition on the secondary cell walls of the vessel elements. Gene expression analyses suggested that PRN2 function is mediated by regulation of the expression of the lignin-biosynthetic genes.

Functional analysis of the heterotrimeric NF-Y transcription factor complex in cassava disease resistance

BACKGROUND AND AIMS

The nuclear factor Y (NF-Y) transcription factor complex is important in plant growth, development and stress response. Information regarding this transcription factor complex is limited in cassava (Manihot esculenta). In this study, 15 MeNF-YAs, 21 MeNF-YBs and 15 MeNF-YCs were comprehensively characterized during plant defence.

METHODS

Gene expression in MeNF-Ys was examined during interaction with the bacterial pathogen Xanthomonas axonopodis pv. manihotis (Xam). The yeast two-hybrid system was employed to investigate protein-protein interactions in the heterotrimeric NF-Y transcription factor complex. The in vivo roles of MeNF-Ys were revealed by virus-induced gene silencing (VIGS) in cassava.

KEY RESULTS

The regulation of MeNF-Ys in response to Xam indicated their possible roles in response to cassava bacterial blight. Protein-protein interaction assays identified the heterotrimeric NF-Y transcription factor complex (MeNF-YA1/3, MeNF-YB11/16 and MeNF-YC11/12). Moreover, the members of the heterotrimeric NF-Y transcription factor complex were located in the cell nucleus and conferred transcriptional activation activity to the CCAAT motif. Notably, the heterotrimeric NF-Y transcription factor complex positively regulated plant disease resistance to Xam, confirmed by a disease phenotype in overexpressing plants in Nicotiana benthamiana and VIGS in cassava. Consistently, the heterotrimeric NF-Y transcription factor complex positively regulated the expression of pathogenesis-related genes (MePRs).

CONCLUSIONS

The NF-Y transcription factor complex (MeNF-YA1/3, MeNF-YB11/16 and MeNF-YC11/12) characterized here was shown to play a role in transcriptional activation of MePR promoters, contributing to the plant defence response in cassava.

Up-regulation of microRNA targets correlates with symptom severity in Citrus sinensis plants infected with two different isolates of citrus psorosis virus

MAIN CONCLUSION: miRNA targets from Citrus sinensis are predicted and validated using degradome data. They show an up-regulation upon infection with CPsV, with a positive correlation between target expression and symptom severity. Sweet orange (Citrus sinensis) may suffer from disease symptoms induced by virus infections, thus resulting in drastic economic losses. Infection of sweet orange plants with two isolates of citrus psorosis virus (CPsV), expressing different symptomatologies, alters the accumulation of a set of endogenous microRNAs (miRNAs). Here, we predicted ten putative targets from four down-regulated miRNAs: three belonging to the CCAAT-binding transcription factor family (CBFAs); an Ethylene-responsive transcription factor (RAP2-7); an Integrase-type DNA-binding superfamily protein (AP2B); Transport inhibitor response 1 (TIR1); GRR1-like protein 1-related (GRR1); Argonaute 2-related (AGO2), Argonaute 7 (AGO7), and a long non-coding RNA (ncRNA). We validated six of them through analysis of leaf degradome data. Expressions of the validated targets increase in infected samples compared to healthy tissue, showing a more striking up-regulation those samples with higher symptom severity. This study contributes to the understanding of the miRNA-mediated regulation of important transcripts in Citrus sinensis through target validation and shed light in the manner a virus can alter host regulatory mechanisms leading to symptom expression.

Last-Generation Genome-Environment Associations Reveal the Genetic Basis of Heat Tolerance in Common Bean (Phaseolus vulgaris L.)

Genome-environment associations (GEAs) are a powerful strategy for the study of adaptive traits in wild plant populations, yet they still lack behind in the use of modern statistical methods as the ones suggested for genome-wide association studies (GWASs). In order to bridge this gap, we couple GEA with last-generation GWAS algorithms in common bean to identify novel sources of heat tolerance across naturally heterogeneous ecosystems. Common bean (Phaseolus vulgaris L.) is the most important legume for human consumption, and breeding it for resistance to heat stress is key because annual increases in atmospheric temperature are causing decreases in yield of up to 9% for every 1°C. A total of 78 geo-referenced wild accessions, spanning the two gene pools of common bean, were genotyped by sequencing (GBS), leading to the discovery of 23,373 single-nucleotide polymorphism (SNP) markers. Three indices of heat stress were developed for each accession and inputted in last-generation algorithms (i.e. SUPER, FarmCPU, and BLINK) to identify putative associated loci with the environmental heterogeneity in heat stress. Best-fit models revealed 120 significantly associated alleles distributed in all 11 common bean chromosomes. Flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Some of these genes were directly linked to heat-responsive pathways, such as the activation of heat shock proteins (MED23, MED25, HSFB1, HSP40, and HSP20). We also found protein domains related to thermostability in plants such as S1 and Zinc finger A20 and AN1. Other genes were related to biological processes that may correlate with plant tolerance to high temperature, such as time to flowering (MED25, MBD9, and PAP), germination and seedling development (Pkinase_Tyr, Ankyrin-B, and Family Glicosil-hydrolase), cell wall stability (GAE6), and signaling pathway of abiotic stress via abscisic acid (histone-like transcription factors NFYB and phospholipase C) and auxin (Auxin response factor and AUX_IAA). This work offers putative associated loci for marker-assisted and genomic selection for heat tolerance in common bean. It also demonstrates that it is feasible to identify genome-wide environmental associations with modest sample sizes by using a combination of various carefully chosen environmental indices and last-generation GWAS algorithms.

Identification, expression, and putative target gene analysis of nuclear factor-Y (NF-Y) transcription factors in tea plant (Camellia sinensis)

Genome-wide identification and characterization of nuclear factor-Y family in tea plants, and their expression profiles and putative targets provide the basis for further elucidation of their biological functions. The nuclear factor-Y (NF-Y) transcription factors (TFs) are crucial regulators of plant growth and physiology. However, the NF-Y TFs in tea plant (Camellia sinensis) have not yet been elucidated, and its biological functions, especially the putative target genes within the genome range, are still unclear. In this study, we identified 35 CsNF-Y encoding genes in the tea plant genome, including 10 CsNF-YAs, 15 CsNF-YBs and 10 CsNF-YCs. Their conserved domains and motifs, phylogeny, duplication event, gene structure, and promoter were subsequently analyzed. Tissue expression analysis revealed that CsNF-Ys exhibited three distinct expression patterns in eight tea tree tissues, among which CsNF-YAs were moderately expressed. Drought and abscisic acid (ABA) treatment indicated that CsNF-YAs may have a greater impact than other subunit members. Furthermore, through the genome-wide investigation of the presence of the CCAAT box, we found that CsNF-Ys may participate in the development of tea plants by regulating target genes of multiple physiological pathways, including photosynthesis, chlorophyll metabolism, fatty acid biosynthesis, and amino acid metabolism pathways. Our findings will contribute to the functional analysis of NF-Y genes in woody plants and the cultivation of high-quality tea plant cultivars.

The Plant NF-Y DNA Matrix In Vitro and In Vivo

Nuclear Factor Y (NF-Y) is an evolutionarily conserved trimer formed by a Histone-Fold Domain (HFD) heterodimeric module shared by core histones, and the sequence-specific NF-YA subunit. In plants, the genes encoding each of the three subunits have expanded in number, giving rise to hundreds of potential trimers. While in mammals NF-Y binds a well-characterized motif, with a defined matrix centered on the CCAAT box, the specificity of the plant trimers has yet to be determined. Here we report that Arabidopsis thaliana NF-Y trimeric complexes, containing two different NF-YA subunits, bind DNA in vitro with similar affinities. We assayed precisely sequence-specificity by saturation mutagenesis, and analyzed genomic DNA sites bound in vivo by selected HFDs. The plant NF-Y CCAAT matrix is different in nucleotides flanking CCAAT with respect to the mammalian matrix, in vitro and in vivo. Our data point to flexible DNA-binding rules by plant NF-Ys, serving the scope of adapting to a diverse audience of genomic motifs.

Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)

Members of the plant Heme Activator Protein (HAP) or NUCLEAR FACTOR Y (NF-Y) are trimeric transcription factor complexes composed of the NF-YA, NF-YB and NF-YC subfamilies. They bind to the CCAAT box in the promoter regions of the target genes and regulate gene expressions. Plant NF-Ys were reported to be involved in adaptation to several abiotic stresses as well as in development. In silico analysis of Sorghum bicolor genome resulted in the identification of a total of 42 NF-Y genes, among which 8 code for the SbNF-YA, 19 for SbNF-YB and 15 for the SbNF-YC subunits. Analysis was also performed to characterize gene structures, chromosomal distribution, duplication status, protein subcellular localizations, conserved motifs, ancestral protein sequences, miRNAs and phylogenetic tree construction. Phylogenetic relationships and ortholog predictions displayed that sorghum has additional NF-YB genes with unknown functions in comparison with Arabidopsis. Analysis of promoters revealed that they harbour many stress-related cis-elements like ABRE and HSE, but surprisingly, DRE and MYB elements were not detected in any of the subfamilies. SbNF-YA1, 2, and 6 were found upregulated under 200 mM salt and 200 mM mannitol stresses. While NF-YA7 appeared associated with high temperature (40°C) stress, NF-YA8 was triggered by both cold (4°C) and high temperature stresses. Among NF-YB genes, 7, 12, 15, and 16 were induced under multiple stress conditions such as salt, mannitol, ABA, cold and high temperatures. Likewise, NF-YC 6, 11, 12, 14, and 15 were enhanced significantly in a tissue specific manner under multiple abiotic stress conditions. Majority of the mannitol (drought)-inducible genes were also induced by salt, high temperature stresses and ABA. Few of the high temperature stress-induced genes are also induced by cold stress (NF-YA2, 4, 6, 8, NF-YB2, 7, 10, 11, 12, 14, 16, 17, NF-YC4, 6, 12, and 13) thus suggesting a cross talk among them. This work paves the way for investigating the roles of diverse sorghum NF-Y proteins during abiotic stress responses and provides an insight into the evolution of diverse NF-Y members.

Genome-wide characterization of the NUCLEAR FACTOR-Y (NF-Y) family in Citrus grandis identified CgNF-YB9 involved in the fructose and glucose accumulation

BACKGROUND

Nuclear factor Y (NF-Y) is increasingly known to be involved in many aspects of plant growth and development. To date, the systematic characterization of NF-Y family has never been reported in Citrus grandis.

OBJECTIVE

Genome-wide characterization of C. grandis NF-Y (CgNF-Y) family and analysis of their role in sucrose metabolism.

METHODS

NF-Y conserved models were employed to identify CgNF-Y genes from genomic data. Phylogenetic tree was generated by the neighbor-joining method using program MEGA 7.0. Based on our previous transcriptomic data, the transcription levels were calculated by RSEM software and were clustered by ShortTime-series Expression Miner. The plant expression vector of CgNF-YB9 was constructed using In-Fusion Cloning and transferred into tobacco by leaf disc transformation method. Soluble sugars and gene expressions were analysis by HPLC and qRT-PCR, respectively.

RESULTS

A total of 24 CgNF-Y genes (6 CgNF-YAs, 13 CgNF-YBs and 5 CgNF-YCs) were identified with conserved domains. Phylogenetic analysis of the NF-Y proteins indicated that NF-YA, NF-YB and NF-YC could be categorized into four, five and three clades, respectively. Expression profiling analysis reflected spatio-temporally distinct expression patterns for CgNF-Y genes. Importantly, we observed a positive correlation between the expression level of CgNF-YB9 and the content of soluble sugar. Moreover, CgNF-YB9-corelated genes were enriched in carbohydrate metabolism. In CgNF-YB9 overexpression lines, sucrose content showed a decrease, whereas glucose and fructose contents displayed an increase. As expected, the transcription levels of sucrose-phosphate synthase and vacuolar invertase in transgenic Line 3 were observed with significantly down- and up-regulated, respectively.

CONCLUSIONS

The structure, phylogenetic relationship and expression pattern of 24 CgNF-Y genes were identified, and CgNF-YB9 was involved in sucrose metabolism.

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.

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.

Emerging themes in heterotrimeric G-protein signaling in plants

Heterotrimeric G-proteins are key signaling components involved during the regulation of a multitude of growth and developmental pathways in all eukaryotes. Although the core proteins (Gα, Gβ, Gγ subunits) and their basic biochemistries are conserved between plants and non-plant systems, seemingly different inherent properties of specific components, altered wirings of G-protein network architectures, and the presence of novel receptors and effector proteins make plant G-protein signaling mechanisms somewhat distinct from the well-established animal paradigm. G-protein research in plants is getting a lot of attention recently due to the emerging roles of these proteins in controlling many agronomically important traits. New findings on both canonical and novel G-protein components and their conserved and unique signaling mechanisms are expected to improve our understanding of this important module in affecting critical plant growth and development pathways and eventually their utilization to produce plants for the future needs. In this review, we briefly summarize what is currently known in plant G-protein research, describe new findings and how they are changing our perceptions of the field, and discuss important issues that still need to be addressed.

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.

A transcriptional view on somatic embryogenesis

Somatic embryogenesis is a form of induced plant cell totipotency where embryos develop from somatic or vegetative cells in the absence of fertilization. Somatic embryogenesis can be induced in vitro by exposing explants to stress or growth regulator treatments. Molecular genetics studies have also shown that ectopic expression of specific embryo‐ and meristem‐expressed transcription factors or loss of certain chromatin‐modifying proteins induces spontaneous somatic embryogenesis. We begin this review with a general description of the major developmental events that define plant somatic embryogenesis and then focus on the transcriptional regulation of this process in the model plant Arabidopsis thaliana (arabidopsis). We describe the different somatic embryogenesis systems developed for arabidopsis and discuss the roles of transcription factors and chromatin modifications in this process. We describe how these somatic embryogenesis factors are interconnected and how their pathways converge at the level of hormones. Furthermore, the similarities between the developmental pathways in hormone‐ and transcription‐factor‐induced tissue culture systems are reviewed in the light of our recent findings on the somatic embryo‐inducing transcription factor BABY BOOM.

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.

Pattern of expression and interaction specificity of multiple G-protein beta (Gβ) subunit isoforms with their potential target proteins reveal functional dominance of BjuGβ1 in the allotetraploid Brassica juncea

Heterotrimeric G-protein, consisting Gα, Gβ and Gγ subunits, interacts with various upstream and downstream effector (target) proteins to regulate a large array of conserved and species-specific biological functions. The targets of G-protein components are recently reported in model plant Arabidopsis thaliana; however limited information is available from crop species. In this study, we utilized yeast two-hybrid (Y2H) assay to screen the diversity of interacting partners of multiple Gβ subunit isoforms from allotetraploid Brassica juncea, a globally important oilseed and vegetable crop. The three BjuGβ genes (BjuGβ1-3), resulted from whole genome triplication event in Brassica lineage, showed distinct expression profile during plant developmental stages with maximal transcript abundance during reproductive stages. Protein-protein interaction of three BjuGβ proteins (bait) against the Y2H cDNA library (prey) identified a total of 14 and 1 non-redundant targets for BjuGβ1 and BjuGβ2, whereas BjuGβ3 screening surprisingly did not yield any genuine target, thereby suggesting functional dominance of BjuGβ1. The triplicated BjuGβ isoforms showed a high degree of interaction strength and specificity with the identified target proteins, which are known to be involved in diverse biological functions in plants. qRT-PCR analysis further indicated that the expression of BjuGβ-target genes was developmentally regulated under various tissue types studied and showed a high degree of co-expression pattern with the BjuGβ genes, particularly during flower and silique development in B. juncea. Taken together, our data provides novel insights on pattern of expression and interaction specificity governing functional divergence of multiple Gβ subunit proteins in polyploid B. juncea.

LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development

LEAFY COTYLEDON1 (LEC1), an atypical subunit of the nuclear transcription factor Y (NF-Y) CCAAT-binding transcription factor, is a central regulator that controls many aspects of seed development including the maturation phase during which seeds accumulate storage macromolecules and embryos acquire the ability to withstand desiccation. To define the gene networks and developmental processes controlled by LEC1, genes regulated directly by and downstream of LEC1 were identified. We compared the mRNA profiles of wild-type and lec1-null mutant seeds at several stages of development to define genes that are down-regulated or up-regulated by the lec1 mutation. We used ChIP and differential gene-expression analyses in Arabidopsis seedlings overexpressing LEC1 and in developing Arabidopsis and soybean seeds to identify globally the target genes that are transcriptionally regulated by LEC1 in planta Collectively, our results show that LEC1 controls distinct gene sets at different developmental stages, including those that mediate the temporal transition between photosynthesis and chloroplast biogenesis early in seed development and seed maturation late in development. Analyses of enriched DNA sequence motifs that may act as cis-regulatory elements in the promoters of LEC1 target genes suggest that LEC1 may interact with other transcription factors to regulate distinct gene sets at different stages of seed development. Moreover, our results demonstrate strong conservation in the developmental processes and gene networks regulated by LEC1 in two dicotyledonous plants that diverged ∼92 Mya.

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.

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.

De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission

Yellow lupine (Lupinus luteus L., Taper c.), a member of the legume family (Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion. Little is known about the molecular network controlling the yellow lupine organ abscission. The aim of our study was to establish the divergences and similarities in transcriptional networks in the pods, flowers and flower pedicels abscised or maintained on the plant, and to identify genes playing key roles in generative organ abscission in yellow lupine. Based on de novo transcriptome assembly, we identified 166,473 unigenes representing 219,514 assembled unique transcripts from flowers, flower pedicels and pods undergoing abscission and from control organs. Comparison of the cDNA libraries from dropped and control organs helped in identifying 1,343, 2,933 and 1,491 differentially expressed genes (DEGs) in the flowers, flower pedicels and pods, respectively. In DEG analyses, we focused on genes involved in phytohormonal regulation, cell wall functioning and metabolic pathways. Our results indicate that auxin, ethylene and gibberellins are some of the main factors engaged in generative organ abscission. Identified 28 DEGs common for all library comparisons are involved in cell wall functioning, protein metabolism, water homeostasis and stress response. Interestingly, among the common DEGs we also found an miR169 precursor, which is the first evidence of micro RNA engaged in abscission. A KEGG pathway enrichment analysis revealed that the identified DEGs were predominantly involved in carbohydrate and amino acid metabolism, but some other pathways were also targeted. This study represents the first comprehensive transcriptome-based characterization of organ abscission in L. luteus and provides a valuable data source not only for understanding the abscission signaling pathway in yellow lupine, but also for further research aimed at improving crop yields.