SHORT HYPOCOTYL UNDER BLUE1 truncations and mutations alter its association with a signaling protein complex in Arabidopsis

The pho1;2a'-m1.1 allele of Phosphate1 conditions misregulation of the phosphorus starvation response in maize (Zea mays ssp. mays L.)

Plant PHO1 proteins play a central role in the translocation and sensing of inorganic phosphate. The maize (Zea mays ssp. mays) genome encodes two co-orthologs of the Arabidopsis PHO1 gene, designated ZmPho1;2a and ZmPho1;2b. Here, we report the characterization of the transposon footprint allele Zmpho1;2a'-m1.1, which we refer to hereafter as pho1;2a. The pho1;2a allele is a stable derivative formed by excision of an Activator transposable element from the ZmPho1;2a gene. The pho1;2a allele contains an 8-bp insertion at the point of transposon excision that disrupts the reading frame and is predicted to generate a premature translational stop. We show that the pho1;2a allele is linked to a dosage-dependent reduction in Pho1;2a transcript accumulation and a mild reduction in seedling growth. Characterization of shoot and root transcriptomes under full nutrient, low nitrogen, low phosphorus, and combined low nitrogen and low phosphorus conditions identified 1100 differentially expressed genes between wild-type plants and plants carrying the pho1;2a mutation. Of these 1100 genes, 966 were upregulated in plants carrying pho1;2a, indicating the wild-type PHO1;2a to predominantly impact negative gene regulation. Gene set enrichment analysis of the pho1;2a-misregulated genes revealed associations with phytohormone signaling and the phosphate starvation response. In roots, differential expression was broadly consistent across all nutrient conditions. In leaves, differential expression was largely specific to low phosphorus and combined low nitrogen and low phosphorus conditions. Of 276 genes upregulated in the leaves of pho1;2a mutants in the low phosphorus condition, 153 were themselves induced in wild-type plants with respect to the full nutrient condition. Our observations suggest that Pho1;2a functions in the fine-tuning of the transcriptional response to phosphate starvation through maintenance and/or sensing of plant phosphate status.

Systems biology-based analysis indicates that PHO1;H10 positively modulates high light-induced anthocyanin biosynthesis in Arabidopsis leaves

Arabidopsis PHO1;H10 is a member of the PHO1 gene family with SPX and EXS domains, and its functions remain largely unknown. As shown in PCSD database, the upstream region of PHO1;H10 gene is in the active chromatin states, with high DHS accessibility and binding sites of multiple transcription factors, especially ABI5, SPCH and HY5. Co-expression network and data-mining analyses showed PHO1;H10 and co-expression genes were with activation under high light stress. We did wet-lab experiments, and found that the detached leaves of PHO1;H10 overexpression lines accumulated more anthocyanin than those of WT and mutant under high light treatment. RNA-seq results showed overexpression of PHO1;H10 up-regulated many anthocyanin biosynthetic genes. The GSEA analysis result showed that the functional module related to anthocyanin pathway was significantly enriched. In summary, we conducted systems biology approach, combining dry- and wet-lab analyses, and discovered that PHO1;H10 might play an essential role during modulating high light-induced anthocyanin accumulation in the Arabidopsis detached leaves.

WRKY2 and WRKY10 regulate the circadian expression of PIF4 during the day through interactions with CCA1/LHY and phyB

WRKY transcription factors are known mostly for their function in plant defense, abiotic stress responses, senescence, seed germination, and development of the pollen, embryo, and seed. Here, we report the regulatory functions of two WRKY proteins in photomorphogenesis and PIF4 expression. PIF4 is a critical signaling hub in light, temperature, and hormonal signaling pathways. Either its expression or its accumulation peaks in the morning and afternoon. WRKY2 and WRKY10 form heterodimers and recognize their target site in the PIF4 promoter near the MYB element that is bound by CCA1 and LHY under red and blue light. WRKY2 and WRKY10 interact directly with CCA1/LHY to enhance their targeting but interact indirectly with SHB1. The two WRKY proteins also interact with phyB, and their interaction enhances the targeting of CCA1 and LHY to the PIF4 promoter. SHB1 associates with the WRKY2 and WRKY10 loci and enhances their expression in parallel with the PIF4 expression peaks. This forward regulatory loop further sustains the accumulation of the two WRKY proteins and the targeting of CCA1/LHY to the PIF4 locus. In summary, interactions of two WRKY proteins with CCA1/LHY and phyB maintain an optimal expression level of PIF4 toward noon and afternoon, which is essential to sketch the circadian pattern of PIF4 expression.

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

BACKGROUND

SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes.

RESULTS

We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs.

CONCLUSION

This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

SHB1 and CCA1 interaction desensitizes light responses and enhances thermomorphogenesis

Light and temperature are two important environmental signals to plants. After dawn, photo-activated phytochromes translocate into the nucleus and interact with a family of negative basic helix-loop-helix PIF regulators. Subsequent phosphorylation and degradation of PIFs triggers a series of photomorphogenic responses. However, excess light can damage the photosynthetic apparatus and leads to photoinhibition. Plants acclimate to a balanced state of photomorphogenesis to avoid photodamage. Here, we show that upregulation of PIF4 expression by SHB1 and CCA1 under red light represents a desensitization step. After dawn, the highly expressed circadian clock protein CCA1 brings circadian signals to the regulatory region of the PIF4 signaling hub. Recruitment of SHB1 by CCA1 modulates red light-specific induction of PIF4 expression thus integrating circadian and light signals. As noon approaches and light intensity and ambient temperature tend to increase, the SHB1–CCA1 interaction sustains PIF4 expression to trigger thermomorphogenic responses to changing light and temperature conditions.

The PIF4 transcription factor promotes adaptation to elevated temperature but is degraded under red light to trigger photomorphogenesis. Here Sun et al. show that the core circadian component CCA1 recruits SHB1 to sustain PIF4 expression after dawn to balance thermomorphogenesis and light responses.

Tobacco rattle virus (TRV)-Mediated Silencing of Nicotiana benthamiana ARGONAUTES (NbAGOs) Reveals New Antiviral Candidates and Dominant Effects of TRV-NbAGO1

The objective of this study was to determine the contribution of different ARGONAUTE proteins in Nicotiana benthamiana (NbAGOs) to the defense against silencing sensitive GFP-expressing viral constructs based on Tomato bushy stunt virus (TBSV) (Tombusvirus), Sunn-hemp mosaic virus (Tobamovirus), and Foxtail mosaic virus (Potexvirus). Upon Tobacco rattle virus (TRV)-mediated down-regulation of NbAGO1, 4, 5, or 6, no effects were noted on susceptibility to any virus construct, whereas knockdown of NbAGO2 specifically prevented silencing of P19-defective TBSV (TGdP19). Down-regulation of a new gene referred to as NbAGO5L showed some reduced silencing for TGdP19 but not for the other two virus constructs, whereas silencing of NbAGO7 gave rise to a subtle increase in susceptibility to all three viruses. Co-infiltrating different TRV-NbAGO constructs simultaneously did not enhance virus susceptibility. However, an unexpected finding was that whenever the TRV-NbAGO1 construct was present, this compromised silencing of genes targeted by co-infiltrated constructs, as shown upon co-infiltration of TRV-NbAGO1 with either TRV-NbAGO2 or TRV-Sul (targeting Magnesium chelatase I). Only after a prolonged period (approximately 2 months) did TRV-Sul-mediated systemic bleaching occur in these co-infected plants, suggesting that TRV-NbAGO1 hinders the silencing ability of other TRV-NbAGO constructs. In conclusion, this study revealed new antiviral NbAGOs and dominant effects of silencing NbAGO1.

Down-regulation of OsSPX1 caused semi-male sterility, resulting in reduction of grain yield in rice

OsSPX1, a rice SPX domain gene, involved in the phosphate (Pi)-sensing mechanism plays an essential role in the Pi-signalling network through interaction with OsPHR2. In this study, we focused on the potential function of OsSPX1 during rice reproductive phase. Based on investigation of OsSPX1 antisense and sense transgenic rice lines in the paddy fields, we discovered that the down-regulation of OsSPX1 caused reduction of seed-setting rate and filled grain number. Through examination of anthers and pollens of the transgenic and wild-type plants by microscopy, we found that the antisense of OsSPX1 gene led to semi-male sterility, with lacking of mature pollen grains and phenotypes with a disordered surface of anthers and pollens. We further conducted rice whole-genome GeneChip analysis to elucidate the possible molecular mechanism underlying why the down-regulation of OsSPX1 caused deficiencies in anthers and pollens and lower seed-setting rate in rice. The down-regulation of OsSPX1 significantly affected expression of genes involved in carbohydrate metabolism and sugar transport, anther development, cell cycle, etc. These genes may be related to pollen fertility and male gametophyte development. Our study demonstrated that down-regulation of OsSPX1 disrupted rice normal anther and pollen development by affecting carbohydrate metabolism and sugar transport, leading to semi-male sterility, and ultimately resulted in low seed-setting rate and grain yield.

Pi sensing and signalling: from prokaryotic to eukaryotic cells

Phosphorus is one of the most important macronutrients and is indispensable for all organisms as a critical structural component as well as participating in intracellular signalling and energy metabolism. Sensing and signalling of phosphate (Pi) has been extensively studied and is well understood in single-cellular organisms like bacteria (Escherichia coli) and Saccharomyces cerevisiae. In comparison, the mechanism of Pi regulation in plants is less well understood despite recent advances in this area. In most soils the available Pi limits crop yield, therefore a clearer understanding of the molecular basis underlying Pi sensing and signalling is of great importance for the development of plants with improved Pi use efficiency. This mini-review compares some of the main Pi regulation pathways in prokaryotic and eukaryotic cells and identifies similarities and differences among different organisms, as well as providing some insight into future research.

Identification of plant vacuolar transporters mediating phosphate storage

Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as PHOSPHATE TRANSPORTER 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on ³¹P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of the rice homologue OsSPX-MFS1 mediates Pi influx to yeast vacuoles. Our findings show that a group of Pi transporters in vacuolar membranes regulate cytoplasmic Pi homeostasis and are required for fitness and plant growth.

The plant vacuole acts as a storage compartment for inorganic phosphate and buffers cytoplasmic phosphate concentration. Here, Liu et al. identify a group of vacuolar phosphate transporters in Arabidopsis that are required for plant growth in response to fluctuating availability of phosphate.

Replace, reuse, recycle: improving the sustainable use of phosphorus by plants

The 'phosphorus problem' has recently received strong interest with two distinct strands of importance. The first is that too much phosphorus (P) is entering into waste water, creating a significant economic and ecological problem. Secondly, while agricultural demand for phosphate fertilizer is increasing to maintain crop yields, rock phosphate reserves are rapidly declining. Unravelling the mechanisms by which plants sense, respond to, and acquire phosphate can address both problems, allowing the development of crop plants that are more efficient at acquiring and using limited amounts of phosphate while at the same time improving the potential of plants and other photosynthetic organisms for nutrient recapture and recycling from waste water. In this review, we attempt to synthesize these important but often disparate parts of the debate in a holistic fashion, since solutions to such a complex problem require integrated and multidisciplinary approaches that address both P supply and demand. Rapid progress has been made recently in our understanding of local and systemic signalling mechanisms for phosphate, and of expression and regulation of membrane proteins that take phosphate up from the environment and transport it within the plant. We discuss the current state of understanding of such mechanisms involved in sensing and responding to phosphate stress. We also discuss approaches to improve the P-use efficiency of crop plants and future direction for sustainable use of P, including use of photosynthetic organisms for recapture of P from waste waters.

Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner

In plants, sensing the levels of external and internal nutrients is essential for reprogramming the transcriptome and adapting to the fluctuating environment. Phosphate (Pi) is a key plant nutrient, and a large proportion of Pi starvation-responsive genes are under the control of Phosphate Starvation Response Regulator 1 (PHR1) in Arabidopsis (AtPHR1) and its homologs, such as Oryza sativa (Os)PHR2 in rice. AtPHR1 and OsPHR2 expression is not very responsive to Pi starvation, raising the question as to how plants sense changes in cellular Pi levels to activate the central regulator. SPX [named after SYG1 (suppressor of yeast gpa1), Pho81 (CDK inhibitor in yeast PHO pathway), and XPR1 (xenotropic and polytropic retrovirus receptor)] proteins that harbor only the SPX domain are reported to be involved in the negative regulation of Pi starvation responses. Here, we show that the nuclear localized SPX proteins SPX1 and SPX2 are Pi-dependent inhibitors of the activity of OsPHR2 in rice. Indeed, SPX1 and SPX2 proteins interact with PHR2 through their SPX domain, inhibiting its binding to P1BS (the PHR1-binding sequence: GNATATNC). In vivo data, as well as results from in vitro experiments using purified SPX1, SPX2, and OsPHR2 proteins, showed that SPX1 and SPX2 inhibition of OsPHR2 activity is Pi-dependent. These data provide evidence to support the involvement of SPX1 and SPX2 in the Pi-sensing mechanism in plants.

Determination of the genetic architecture of seed size and shape via linkage and association analysis in soybean (Glycine max L. Merr.)

Seed-size traits, which are controlled by multiple genes in soybean, play an important role in determining seed yield, quality and appearance. However, the molecular mechanisms controlling the size of soybean seeds remain unclear, and little research has been done to investigate these mechanisms. In this study, we performed a genetic analysis to determine the genetic architecture of soybean seed size and shape via linkage and association analyses. We used 184 recombinant inbred lines (RILs) and 219 cultivated soybean accessions to evaluate seed length, seed width and seed height as seed-size traits, and their ratios of these values as seed-shape traits. Our results showed that all six traits had high heritability ranging from 92.46 to 98.47 %. Linkage analysis in the RILs identified 12 quantitative traits loci (QTLs), with five of these QTLs being associated with seed size, five with seed shape and two with the two first principal components of our principal component analysis (PCA). Association analysis in the 219 accessions detected 41 single nucleotide polymorphism (SNP)-trait associations, with 20 of these SNPs being associated with seed-size traits, seven with seed-shape traits and 14 with the two first principal components of our PCA. This analysis reveals that seed-size and seed-shape may be controlled by different genetic factors. Our results provide a greater understanding of phenotypic structure and genetic architecture of soybean seed, and the QTLs detected in this study form a basis for future fine mapping, quantitative trait gene cloning and molecular breeding in soybean.

Phylogeny, structural evolution and functional diversification of the plant PHOSPHATE1 gene family: a focus on Glycine max

BACKGROUND

PHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. Therefore, we surveyed the evolutionary patterns of genomes within the plant PHO1 gene family, focusing on soybean (Glycine max) due to its economic importance.

RESULTS

Our data show that PHO1 genes could be classified into two major groups (Class I and Class II). Class I genes were only present and expanded in dicotyledonous plants and Selaginella moellendorffii; Class II genes were found in all land plants. Class I sequence losses in other lineages may be attributed to gene loss after duplication events in land plant evolution. Introns varied from 7 to 14, and ancestral state reconstruction analyses revealed that genes with 13 introns were ancestral, thus suggesting that the intron loss was a chief constituent of PHO1 gene evolution. In the soybean genome, only 12 PHO1-like genes (GmaPHO1) were detected at the mRNA level. These genes display tissue-specific or tissue-preferential expression patterns during soybean plant and fruit development. Class I genes were more broadly expressed than Class II. GmaPHO1 genes had altered expression in response to salt, osmotic, and inorganic phosphate stresses.

CONCLUSIONS

Our study revealed that PHO1 genes originated from a eukaryotic ancestor and that two major classes formed in land plants. Class I genes are only present in dicots and lycophytes. GmaPHO1genes had diverse expression patterns in soybean, indicating their dramatic functional diversification.

De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana

BACKGROUND

Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection.

METHODOLOGY/RESULTS

RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of 16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription.

CONCLUSIONS

The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant.

A WRKY transcription factor recruits the SYG1-like protein SHB1 to activate gene expression and seed cavity enlargement

Seed development in Arabidopsis and in many dicots involves an early proliferation of the endosperm to form a large embryo sac or seed cavity close to the size of the mature seed, followed by a second phase during which the embryo grows and replaces the endosperm. SHORT HYPOCOTYL UNDER BLUE1 (SHB1) is a member of the SYG1 protein family in fungi, Caenorhabditis elegans, flies, and mammals. SHB1 gain-of-function enhances endosperm proliferation, increases seed size, and up-regulates the expression of the WRKY transcription factor gene MINISEED3 (MINI3) and the LRR receptor kinase gene HAIKU2 (IKU2). Mutations in either IKU2 or MINI3 retard endosperm proliferation and reduce seed size. However, the molecular mechanisms underlying the establishment of the seed cavity and hence the seed size remain largely unknown. Here, we show that the expression of MINI3 and IKU2 is repressed before fertilization and after 4 days after pollination (DAP), but is activated by SHB1 from 2 to 4 DAP prior to the formation of the seed cavity. SHB1 associates with their promoters but without a recognizable DNA binding motif, and this association is abolished in mini3 mutant. MINI3 binds to W-boxes in, and recruits SHB1 to, its own and IKU2 promoters. Interestingly, SHB1, but not MINI3, activates transcription of pMINI3::GUS or pIKU2::GUS. We reveal a critical developmental switch through the activation of MINI3 expression by SHB1. The recruitment of SHB1 by MINI3 to its own and IKU2 promoters represents a novel two-step amplification to counter the low expression level of IKU2, which is a trigger for endosperm proliferation and seed cavity enlargement.

Seed development in many dicots is characterized by a rapid proliferation of the endosperm and growth of integument to form a large embryo sac or seed cavity. In Arabidopsis, the seed cavity is generated at the globular stage or 4 days after pollination. The subsequent growth of the embryo replaces the endosperm during the second phase. Therefore, the volume of the initial seed cavity correlates closely with the final seed size. In shb1-D, an even larger seed cavity is created at 4 DAP due to an up-regulated expression of MINI3 and IKU2 by SHB1. We report that the expression of MINI3 and IKU2 coincides with the formation of the seed cavity. SHB1 is anchored to these promoters by MINI3 to activate their expression in a W-box-dependent manner. Spatiotemporal regulation of gene expression is a crucial mechanism that controls embryo development in many organisms. This interaction of SHB1 with MINI3 should impact studies of their homologs in many other organisms, including humans. Seed development in major seed crops, such as soybean and canola, follows a very similar path to that of Arabidopsis. Our results should lead to an increase in agricultural yields and concomitant increases in the proteins and oil content per seed.

Hypersensitive to red and blue 1 and its modification by protein phosphatase 7 are implicated in the control of Arabidopsis stomatal aperture

The stomatal pores are located on the plant leaf epidermis and regulate CO(2) uptake for photosynthesis and the loss of water by transpiration. Their stomatal aperture therefore affects photosynthesis, water use efficiency, and agricultural crop yields. Blue light, one of the environmental signals that regulates the plant stomatal aperture, is perceived by the blue/UV-A light-absorbing cryptochromes and phototropins. The signal transduction cascades that link the perception of light to the stomatal opening response are still largely unknown. Here, we report two new players, Hypersensitive to Red and Blue 1 (HRB1) and Protein Phosphatase 7 (PP7), and their genetic and biochemical interactions in the control of stomatal aperture. Mutations in either HRB1 or PP7 lead to the misregulation of the stomatal aperture and reduce water loss under blue light. Both HRB1 and PP7 are expressed in the guard cells in response to a light-to-dark or dark-to-light transition. HRB1 interacts with PP7 through its N-terminal ZZ-type zinc finger motif and requires a functional PP7 for its stomatal opening response. HRB1 is phosphorylated in vivo, and PP7 can dephosphorylate HRB1. HRB1 is mostly dephosphorylated in a protein complex of 193 kDa in the dark, and blue light increases complex size to 285 kDa. In the pp7 mutant, this size shift is impaired, and HRB1 is predominately phosphorylated. We propose that a modification of HRB1 by PP7 under blue light is essential to acquire a proper conformation or to bring in new components for the assembly of a functional HRB1 protein complex. Guard cells control stomatal opening in response to multiple environmental or biotic stimuli. This study may furnish strategies that allow plants to enjoy the advantages of both constitutive and ABA-induced protection under water-limiting conditions.

The emerging importance of the SPX domain-containing proteins in phosphate homeostasis

Plant growth and development are strongly influenced by the availability of nutrients in the soil solution. Among them, phosphorus (P) is one of the most essential and most limiting macro-elements for plants. In the environment, plants are often confronted with P starvation as a result of extremely low concentrations of soluble inorganic phosphate (Pi) in the soil. To cope with these conditions, plants have developed a wide spectrum of mechanisms aimed at increasing P use efficiency. At the molecular level, recent studies have shown that several proteins carrying the SPX domain are essential for maintaining Pi homeostasis in plants. The SPX domain is found in numerous eukaryotic proteins, including several proteins from the yeast PHO regulon, involved in maintaining Pi homeostasis. In plants, proteins harboring the SPX domain are classified into four families based on the presence of additional domains in their structure, namely the SPX, SPX-EXS, SPX-MFS and SPX-RING families. In this review, we highlight the recent findings regarding the key roles of the proteins containing the SPX domain in phosphate signaling, as well as providing further research directions in order to improve our knowledge on P nutrition in plants, thus enabling the generation of plants with better P use efficiency.

Phosphate homeostasis in the yeast Saccharomyces cerevisiae, the key role of the SPX domain-containing proteins

In the yeast Saccharomyces cerevisiae, a working model for nutrient homeostasis in eukaryotes, inorganic phosphate (Pi) homeostasis is regulated by the PHO pathway, a set of phosphate starvation induced genes, acting to optimize Pi uptake and utilization. Among these, a subset of proteins containing the SPX domain has been shown to be key regulators of Pi homeostasis. In this review, we summarize the recent progresses in elucidating the mechanisms controlling Pi homeostasis in yeast, focusing on the key roles of the SPX domain-containing proteins in these processes, as well as describing the future challenges and opportunities in this fast-moving field.

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

The congruent development of computational technology, bioinformatics and analytical instrumentation makes proteomics ready for the next leap. Present-day state of the art proteomics grew from a descriptive method towards a full stake holder in systems biology. High throughput and genome wide studies are now made at the functional level. These include quantitative aspects, functional aspects with respect to protein interactions as well as post translational modifications and advanced computational methods that aid in predicting protein function and mapping these functionalities across the species border. In this review an overview is given of the current status of these aspects in plant studies with special attention to non-genomic model plants.

DBB1a, involved in gibberellin homeostasis, functions as a negative regulator of blue light-mediated hypocotyl elongation in Arabidopsis

Double B-box 1a (DBB1a) belongs to the zinc-finger family proteins in Arabidopsis thaliana. Transcriptional analysis uncovered that the DBB1a gene expression was blue light-dependently regulated, and the transcript level of DBB1a in cry1cry2 was decreased but not in phyAphyB compared to wild type under blue light conditions. Transgenic plants containing pDBB1a:GUS (β-glucuronidase) displayed GUS activity in the vascular system of leaves and petioles. Green fluorescent protein (GFP)-fused DDB1a (DBB1a-GFP) protein was found in the nucleus in transient transformation assays with onion epidermal cells as well as in stable transgenic Arabidopsis plants. To investigate the function of DBB1a, we generated DBB1a over-expressing and under-expressing transgenic Arabidopsis plants. Analysis of hypocotyl growth of these lines indicated that DBB1a promoted hypocotyl elongation under blue light condition. The phenotype of transgenic plants with DBB1a over-expression could be impaired by a gibberellin (GA)-biosynthesis inhibitor. Moreover, the expression analysis of GA metabolic and catabolic genes in DBB1a transgenic lines indicated that the DBB1a suppressed GA2-oxidase1 (GA2ox1) and GA2-oxidase8 (GA2ox8) expression, but induced GA3β-hydroxygenase1 (GA3ox1) and GA20-oxidase1 (GA20ox1) expression under blue light. Taken together, we concluded that DBB1a promotes hypocotyl elongation under blue light condition through an increase in bioactive GA levels in Arabidopsis.

HYPOSENSITIVE TO LIGHT, an alpha/beta fold protein, acts downstream of ELONGATED HYPOCOTYL 5 to regulate seedling de-etiolation

Ambient light has profound effects on early seedling de-etiolation through red and far-red light-absorbing phytochromes and blue and UV-A light-absorbing cryptochromes. Subsequent integration of various light signal transduction pathways leads to changes in gene expression and morphogenic responses. Here, we report the isolation of a new Arabidopsis light-signaling component, HYPOSENSITIVE TO LIGHT or HTL. Both htl-1 and htl-2 alleles displayed a long hypocotyl phenotype under red, far-red, and blue light, whereas overexpression of HTL caused a short hypocotyl phenotype under similar light conditions. The mutants also showed other photomorphogenic defects such as elongated petioles, retarded cotyledon and leaf expansion, reduced accumulation of chlorophyll and anthocyanin pigments, and attenuated expression of light-responsive CHLOROPHYLL A/B BINDING PROTEIN 3 and CHALCONE SYNTHASE genes. HTL belongs to an alpha/beta fold protein family and is localized strongly in the nucleus and weakly in the cytosol. The expression of HTL was strongly induced by light of various wavelengths and this light induction was impaired in elongated hypocotyl 5. HY5 directly bound to both a C/G-box and a G-box in the HTL promoter but with a greater affinity toward the C/G-box. HTL, therefore, represents a new signaling step downstream of HY5 in phy- and cry-mediated de-etiolation responses.

Family life at close quarters: communication and constraint in angiosperm seed development

The formation of viable angiosperm seeds involves the co-ordinated growth and development of three genetically distinct organisms, the maternally derived seed coat and the zygotic embryo and endosperm. The physical relationships of these tissues are initially established during the specification and differentiation of the female gametophyte within the tissues of the developing ovule. The molecular programmes implicated in both ovule and seed development involve elements of globally important pathways (such as auxin signalling), as well as ovule- and seed-specific pathways. Recurrent themes, such as the precisely controlled death of specific cell types and the regulation of cell-cell communication and nutrition by the selective establishment of symplastic and apoplastic barriers, appear to play key roles in both pre- and post-fertilization seed development. Much of post-fertilization seed growth occurs during a key developmental window shortly after fertilization and involves the dramatic expansion of the young endosperm, constrained by surrounding maternal tissues. The complex tissue-specific regulation of carbohydrate metabolism in specific seed compartments has been shown to provide a driving force for this early seed expansion. The embryo, which is arguably the most important component of the seed, appears to be only minimally involved in early seed development. Given the evolutionary and agronomic importance of angiosperm seeds, the complex combination of communication pathways which co-ordinate their growth and development remains remarkably poorly understood.