Cell Ablation Reveals That Expression from the Phaseolin Promoter Is Confined to Embryogenesis and Microsporogenesis

Ultramicroscopic examination of mature massulae of Habenaria arinaria (Orchidaceae)

The mature massula of H. arinaria was examined by means of transmission electron microscopy, with the aim to understand the nature of cohesion between grains, the accumulation of pollen storage reserves, and the behavior of the nucleus of the vegetative cell in this composite type of pollen. The massula was a union of a large number of polygonal pollen grains that were tightly linked together. The exine within the massula were highly simplified, consisting of a single layer of nexine-2, lacking tectum, bacula, and nexine-1, while all the four layers comprised the exine on the massula surface. The two layers of nexine-2 of adjacent grains fused into a seamless whole. Undoubtedly the fusion of the nexine-2 was the mechanism by which the grains of the massula were linked together. No starch grains, lipid bodies, or storage proteins were present in the mature massula, and so the composite pollen of this species belonged to a novel type with regard to storage reserves. The vegetative nucleus was not lobed and revealed a huge amount of highly condensed chromatin, indicating a quiescent status. The condensed status of the vegetative nuclei in this composite type of pollen system is in striking contrast to the highly decondensed status reported in the free type of pollen grains.

Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis

The complete lack of seed storage protein expression in vegetative tissues and robust expression during embryogenesis makes seed development an ideal system to study tissue-specific expression of genes. The promoter for the Phaseolin (phas) gene, which encodes the major seed storage protein in bean (Phaseolus vulgaris), is activated in two sequential steps: Phaseolus vulgaris ABI3-like factor (Pv-ALF)-dependent potentiation and abscisic acid-mediated activation. In this study, a heterologous in vivo Pv-ALF/phas-GUS (for β-glucuronidase) expression system in transgenic Arabidopsis thaliana leaves was used in conjunction with the powerful RNA-Seq approach to capture transcriptional landscapes of phas promoter expression. Remarkably, expression of over 1300 genes from 11 functional categories coincided with changes in the transcriptional status of the phas promoter. Gene network analysis of induced genes and artificial microRNA-mediated loss-of-function genetic assays identified transcriptional regulators RINGLET 2 (RLT2) and AINTEGUMENTA-LIKE 5 (AIL5) as being essential for phas transcription. Pv-ALF binding to the RLT2 and AIL5 promoter regions was confirmed by electrophoretic mobility shift assay. RLT2 and AIL5 knockdown lines displayed reduced expression of several endogenous seed genes, suggesting that these factors are involved in activation of endogenous Arabidopsis seed storage gene expression. Overall, the identification of these key factors involved in phas activation provides important insight into the two-step transcriptional regulation of seed-specific gene expression.

Characterization of the mannan synthase promoter from guar (Cyamopsis tetragonoloba)

Guar seed gum, consisting primarily of a high molecular weight galactomannan, is the most cost effective natural thickener, having broad applications in the food, cosmetics, paper, pharmaceutical and petroleum industries. The properties of the polymer can potentially be enhanced by genetic modification. Development of suitable endosperm-specific promoters for use in guar is desirable for metabolic engineering of the seed gum. A ~1.6 kb guar mannan synthase (MS) promoter region has been isolated. The MS promoter sequence was fused with the GUS reporter gene and overexpressed in the heterologous species alfalfa (Medicago sativa). The potential strength and specificity of the MS promoter was compared with those of the constitutive 35S promoter and the seed specific β-phaseolin promoter. Quantitative GUS assays revealed that the MS promoter directs GUS expression specifically in endosperm in transgenic alfalfa. Thus, the guar MS promoter could prove generally useful for directing endosperm-specific expression of transgenes in legume species.

Epigenetic regulation of peanut allergen gene Ara h 3 in developing embryos

Peanut (Arachis hypogaea) allergy is one of the most serious food allergies. Peanut seed protein, Ara h 3, is considered to be one of the most important peanut allergens. Little is known about the temporal and spatial regulation mechanism of Ara h 3 during seed development. In this study, chromatin structure of the Ara h 3 promoter was analyzed to examine its transcriptional regulation. Analysis of transgenic plants of Arabidopsis thaliana expressing Arah3: GUS showed that the Ara h 3 promoter could efficiently direct the seed-specific expression of the GUS reporter gene. Chromatin immunoprecipitation revealed that nucleosomes were depleted at the core promoter of the Ara h 3 upon full activation in the late stage of embryo maturation, which was accompanied by a dramatic decrease of histone acetylation. However, in the early stage of embryo maturation, histone H3 hyperacetylation at the core promoter of Ara h 3 was detected. A decrease of histone H3-K9 dimethylation levels at core promoter of Ara h 3 was also observed with concomitant repression of Ara h 3 in the vegetative tissues. Our results suggest that the histone modification status of Ara h 3 undergoes targeted changes including the increase of histone H3 acetylation and decrease of histone H3-K9 dimethylation in early maturation embryos. In addition, the loss of histone H3 from the proximal promoter of Ara h 3 is associated with its high expression during late embryo maturation.

Overexpression of serine acetlytransferase produced large increases in O-acetylserine and free cysteine in developing seeds of a grain legume

There have been many attempts to increase concentrations of the nutritionally essential sulphur amino acids by modifying their biosynthetic pathway in leaves of transgenic plants. This report describes the first modification of cysteine biosynthesis in developing seeds; those of the grain legume, narrow leaf lupin (Lupinus angustifolius, L.). Expression in developing lupin embryos of a serine acetyltransferase (SAT) from Arabidopsis thaliana (AtSAT1 or AtSerat 2;1) was associated with increases of up to 5-fold in the concentrations of O-acetylserine (OAS), the immediate product of SAT, and up to 26-fold in free cysteine, resulting in some of the highest in vivo concentrations of these metabolites yet reported. Despite the dramatic changes in free cysteine in developing embryos of SAT overexpressers, concentrations of free methionine in developing embryos, and the total cysteine and methionine concentrations in mature seeds were not significantly altered. Pooled F(2) seeds segregating for the SAT transgene and for a transgene encoding a methionine- and cysteine-rich sunflower seed storage protein also had increased OAS and free cysteine, but not free methionine, during development, and no increase in mature seed total sulphur amino acids compared with controls lacking SAT overexpression. The data support the view that the cysteine biosynthetic pathway is active in developing seeds, and indicate that SAT activity limits cysteine biosynthesis, but that cysteine supply is not limiting for methionine biosynthesis or for storage protein synthesis in maturing lupin embryos in conditions of adequate sulphur nutrition. OAS and free methionine, but not free cysteine, were implicated as signalling metabolites controlling expression of a gene for a cysteine-rich seed storage protein.

An epigenetic perspective on developmental regulation of seed genes

The developmental program of seeds is promoted by master regulators that are expressed in a seed-specific manner. Ectopic expression studies reveal that expression of these master regulators and other transcriptional regulators is sufficient to promote seed-associated traits, including generation of somatic embryos. Recent work highlights the importance of chromatin-associated factors in restricting expression of seed-specific genes, in particular PcG proteins and ATP-dependent remodelers. This review summarizes what is known regarding factors that promote zygotic and/or somatic embryogenesis and the chromatin machinery that represses their expression. Characterization of the regulation of seed-specific genes reveals that plant chromatin-based repression systems exhibit broad conservation with and surprising differences from animal repression systems.

The Arabidopsis BRAHMA chromatin-remodeling ATPase is involved in repression of seed maturation genes in leaves

Synthesis and accumulation of seed storage proteins (SSPs) is an important aspect of the seed maturation program. Genes encoding SSPs are specifically and highly expressed in the seed during maturation. However, the mechanisms that repress the expression of these genes in leaf tissue are not well understood. To gain insight into the repression mechanisms, we performed a genetic screen for mutants that express SSPs in leaves. Here, we show that mutations affecting BRAHMA (BRM), a SNF2 chromatin-remodeling ATPase, cause ectopic expression of a subset of SSPs and other embryogenesis-related genes in leaf tissue. Consistent with the notion that such SNF2-like ATPases form protein complexes in vivo, we observed similar phenotypes for mutations of AtSWI3C, a BRM-interacting partner, and BSH, a SNF5 homolog and essential SWI/SNF subunit. Chromatin immunoprecipitation experiments show that BRM is recruited to the promoters of a number of embryogenesis genes in wild-type leaves, including the 2S genes, expressed in brm leaves. Consistent with its role in nucleosome remodeling, BRM appears to affect the chromatin structure of the At2S2 promoter. Thus, the BRM-containing chromatin-remodeling ATPase complex involved in many aspects of plant development mediates the repression of SSPs in leaf tissue.

Ordered histone modifications are associated with transcriptional poising and activation of the phaseolin promoter

The phaseolin (phas) promoter drives copious production of transcripts encoding the protein phaseolin during seed embryogenesis but is silent in vegetative tissues, in which a nucleosome is positioned over its three-phased TATA boxes. Transition from the inactive state in transgenic Arabidopsis thaliana leaves was accomplished by ectopic expression of the transcription factor Phaseolus vulgaris ABI3-like factor (ALF) and application of abscisic acid (ABA). Placement of hemagglutinin-tagged ALF expression under the control of an estradiol-inducible promoter permitted chromatin immunoprecipitation analysis of chronological changes in histone modifications, notably increased acetylation of H3-K9 and H4-K12, as phas chromatin was remodeled (potentiated). A different array of changes, including acetylation of H3-K14 and methylation of H3-K4, was found to be associated with ABA-mediated activation. Thus, temporal separation of phas potentiation from activation revealed that histone H3 and H4 Lys residues are not globally hyperacetylated during phas expression. Whereas decreases in histone H3 and H4 levels were detected during ALF-mediated remodeling, slight increases occurred after ABA-mediated activation, suggesting the restoration of histone-phas interactions or the replacement of histones in the phas chromatin. The observed histone modifications provide insight into factors involved in the euchromatinization and activation of a plant gene and expand the evidence for histone code conservation among eukaryotes.

High rooting frequency and functional analysis of GUS and GFP expression in transgenic Medicago truncatula A17

•  An effective transformation method is described for Medicago truncatula A17, verifying its suitability as a model legume for functional genomics. •  Media and culture methods are detailed that yielded an average frequency of 35% for recovery of transgenic shoots from cotyledonary node explants and 39% for root induction and regeneration of entire plants from 419 phosphinothricin-resistant shoots. •  Fertile plants transgenic for both 35S-GFP and phas-GUS were obtained in five of eight independent experiments. The presence and stable inheritance of transgenes was confirmed by GFP or GUS expression and by genomic DNA blots. GFP expression driven by the normally constitutive CaMV 35S promoter diminished as the leaves matured. Although GUS was very strongly and uniformly expressed in seed cotyledons of most lines, one line exhibited an aberrant, patchy pattern. Additionally, weak GUS expression was evident in leaf veins from the normally stringently spatially regulated phas promoter. •  Stably transformed, fertile, M. truncatula A17 plants were generated. The unconventional expression patterns for 35S-GFP and phas-GUS expression obtained in some transformants suggest the occurrence of novel epigenetic events.

S phase progression is required for transcriptional activation of the beta-phaseolin promoter

Elucidating the mechanisms by which the transcription machinery accesses promoters in their chromatin environment is a fundamental aspect of understanding gene regulation. The phas promoter is normally constrained by a rotationally and translationally positioned nucleosome over its TATA region except during embryogenesis when it is potentiated by the presence of Phaseolus vulgaris ABI3-like factor (PvALF), a plant-specific transcription factor, and activated by an abscisic acid (ABA)-induced signal transduction cascade. Ectopic expression of PvALF and the supply of ABA in transgenic tobacco or Arabidopsis leaves can activate expression from phas. We confirmed by [3H]thymidine incorporation that active DNA replication occurred concomitant with the presence of PvALF and ABA. Arrest of DNA synthesis or S phase progression by infiltration of the leaves with replication inhibitors (hydroxyurea, roscovitine, mimosine) strongly inhibited transcriptional activation, especially the ABA-mediated activation step. Similarly, activation of endogenous Arabidopsis MAT and LEA genes in leaf tissue by the presence of ABA and ectopically expressed PvALF was inhibited by DNA replication arrest. No change in transcript levels on the arrest of replication was detected for abi1, abi2, and era1, negative regulators of the ABA signal transduction cascade or for cell cycle components ick1 and aip3. However, a reduction in transcript accumulation for the crucial ABA signaling effector, abi5, occurred upon DNA replication arrest (probably reflected in the decrease in MAT and LEA gene expression). Contrary to the conventional view that ABA inhibits DNA replication, our findings show that ABA acts in concert with S phase progression to activate gene expression.

Module-specific regulation of the beta-phaseolin promoter during embryogenesis

The phas promoter displays stringent spatial regulation, being very highly expressed during embryogenesis and completely silent during all phases of vegetative development in bean, Phaseolus vulgaris. This pattern is maintained in transgenic tobacco and, as shown here, Arabidopsis. Dimethyl sulphate in vivo footprinting analyses revealed that over 20 cis-elements within the proximal 295 bp of the phas promoter are protected by factor binding in seed tissues whereas none are bound in leaves. The hypothesis that this complex profile represents a summation of several module (cotyledon, hypocotyl, and radicle)-specific factor-DNA interactions has been explored by the incorporation of site-directed substitution mutations into 10 locations within the -295phas promoter. Only 2.6% of -295phas promoter activity remained after mutation of the G-box; the CCAAAT box, the E-box and the RY elements were also found to mediate high levels of expression in embryos. Whereas the CACA element has dual positive and negative regulatory roles, the vicilin box was identified as a strong negative regulatory element. The proximal (-70 to -64) RY motif was found to bestow expression in the hypocotyl while all the RY elements contribute to expression in cotyledons but not to vascular tissue expression during embryogenesis. RY elements at positions -277 to -271, -260 to -254, and -237 to -231 were found to orchestrate radicle-specific repression. The G-box appears to be the functional abscisic acid responsive element and the E-site may be a coupling element. The results substantiate the concept that autarkical cis-element functions generate modular patterning during embryogenesis. They also reflect the existence of both redundancy and hierarchy in cis-element interactions. Importantly, the virtually identical expression patterns observed for the two distantly related plants studied argue strongly for the generality of function for the observed factor-element interactions.

Cre recombinase expression can result in phenotypic aberrations in plants

The cre recombinase gene was stably introduced and expressed in tomato, petunia and Nicotiana tabacum. Some plants expressing the cre gene driven by a CaMV 35S promoter displayed growth retardation and a distinct pattern of chlorosis in their leaves. Although no direct relation can be proven between the phenotype and cre expression, aberrant phenotypes always co-segregate with the transgene, which strongly suggests a correlation. The severity of the phenotype does not correlate with the level of steady-state mRNA in mature leaves, but with the timing of cre expression during organogenesis. The early onset of cre expression in tomato is correlated with a more severe phenotype and with higher germinal transmission frequencies of site-specific deletions. No aberrant phenotype was observed when a tissue-specific phaseolin promoter was used to drive the cre gene. The data suggest that for the application of recombinases in plants, expression is best limited to specific tissues and a short time frame.

Temporal and tissue-specific expression of the tobacco ntf4 MAP kinase

The large number of mitogen-activated protein (MAP) kinase genes identified to date in plants suggests that their encoded proteins have a wide array of functions in development and physiological responses, as has been indicated by studies on the factors which lead to the activation of these kinases. Signalling pathways involving members of a multigene family employ a variety of mechanisms to ensure response specificity, one of which is via differential gene expression. We have performed detailed analyses of the expression of the tobacco ntf4 MAP kinase gene using a variety of approaches. The ntf4 gene promoter region was isolated and a chimeric ntf4 promoter-GUS fusion construct was introduced into plants. GUS expression was detected in pollen, in developing and mature embryos, and shortly after seed germination, but not in other floral tissues and tissues such as leaf, root, or stem. This expression pattern was confirmed by northern and western analyses. In situ hybridization and immunolocalization studies showed that the expression of the ntf4 gene and its encoded protein p45Ntf4 occurred in embryos at least from the globular embryo stage until the mature seed, as well as in the seed endosperm. Taken together, the results show that the p45Ntf4 MAP kinase has a very restricted expression pattern, being found only in pollen and seeds. These findings should be important when considering MAP kinase function in plants.

De novo activation of the beta-phaseolin promoter by phosphatase or protein synthesis inhibitors

The promoter for the phaseolin (phas) bean seed protein gene adopts an inactive chromatin structure in leaves of transgenic tobacco. This repressive architecture, which confers stringent spatial regulation, is disrupted upon transcriptional activation during embryogenesis in a process that requires the presence of both a transcription factor (PvALF) and abscisic acid (ABA). Toward determining the need for de novo synthesis of proteins other than PvALF in transcriptional activation we explored the effect of several eukaryotic protein synthesis inhibitors. Surprisingly, cycloheximide (CHX), emetine, and verrucarin A were able to induce transcription from the phas promoter in tobacco and bean leaf tissue in the absence of either PvALF or ABA. This induction was decreased by the replication inhibitors hydroxyurea and aphidicolin but not by genistein or mimosine. Since protein phosphatases and kinases are essential components of the ABA signal transduction pathway, it is conceivable that CHX is also capable of inducing phosphorylation of proteins usually involved in ABA-mediated activation. Interestingly, okadaic acid, an inhibitor of serine/threonine phosphatase, also strongly activated transcription from the phas promoter. In contrast, the protein synthesis inhibitors anisomycin and puromycin did not activate transcription from the phas promoter, nor did the tyrosine phosphatase inhibitors phenylarsine oxide and sodium orthovanadate. These discrete but different results on transcriptional activation may reflect specific modes of action of the inhibitors, or they may reflect differential interactions of the inhibitors or of downstream events resulting from inhibitor activity with presently unknown components of the transcriptional activation system.

Footprinting in vivo reveals changing profiles of multiple factor interactions with the beta-phaseolin promoter during embryogenesis

Whereas in vitro techniques are essentially limited to the analysis of interactions with a single or limited number of cis-elements, in vivo footprinting techniques can be used to assess the total profile of factor interactions with a promoter. By probing with dimethylsulphate and using sensitive ligation-mediated PCR analytical techniques, the in vivo status of the phas promoter was determined in transcriptionally active (embryo) and inactive (leaf) tissues. Changes in factor occupancy were detected during embryogenesis, and the greatest complexity seen (at mid-maturation) was in accordance with the many potential binding sites predicted on the basis of sequence comparison. Evidence was obtained that several cis-elements not previously shown to be used for factor binding in plant promoters are occupied. The great complexity of footprints may represent the need for multiple factor interaction to achieve high levels of transcription. Alternatively, it is possible that the differential levels of expression in individual regions of the embryo evident from histochemical analysis of the GUS reporter result from the interaction of relatively few factors, with the overall footprinting pattern representing a summation of patterns from various tissues.

Genetic ablation of flowers in transgenic Arabidopsis

We have created transgenic Arabidopsis plants in which a gene encoding the cell-autonomous diphtheria toxin A chain (DT-A) was expressed under the control of the LEAFY (LFY) promoter. This promoter is active both in emerging leaf primordia and young flowers, with the highest activity in flowers. The majority of LFY::DT-A plants had normal vegetative development but lacked flowers, demonstrating that relatively widespread activity of a promoter does not exclude its possible use for ablating selected tissues, as long as differences in activity levels between different tissues are significant. We also found that flowers were replaced by empty bracts in LFY::DT-A plants, suggesting that flower-derived signals normally suppress bract development in Arabidopsis.

Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation

Extensive studies of the beta-phaseolin (phas) gene in transgenic tobacco have shown that it is highly active during seed embryogenesis but is completely silent in leaf and other vegetative tissues. In vivo footprinting revealed that the lack of even basal transcriptional activity in vegetative tissues is associated with the presence of a nucleosome that is rotationally positioned with base pair precision over three phased TATA boxes present in the phas promoter. Positioning is sequence-dependent because an identical rotational setting is obtained upon nucleosome reconstitution in vitro. A comparison of DNase I and dimethyl sulfate footprints in vivo and in vitro strongly suggests that this repressive chromatin architecture is remodeled concomitant with gene activation in the developing seed. This leads to the disruption of histone-mediated DNA wrapping and the assembly of the TATA boxes into a transcriptionally competent nucleoprotein complex.

A 68 bp element of the beta-phaseolin promoter functions as a seed-specific enhancer

In beans, expression of the beta-phaseolin gene (phas), encoding the major seed storage protein of bean (Phaseolus vulgaris) is confined to the cotyledons of developing embryos. Phaseolin has not been detected in the endosperm, which remains liquid and is lost early in development. However, fusion constructs between the phas promoter and the gus-coding region yield expression in both embryo and endosperm of developing seeds from transgenic tobacco (Nicotiana tabacum) plants. Although elements extending 1470 bp upstream of the transcription start site are known to modulate phas expression, the proximal 295 bp (p295) are sufficient to drive high levels of seed-specific GUS activity. This region was dissected into three elements: a 68 bp element (seed specific enhancer, SSE: -295 to -227), a middle region (-227 to -109) and a basal phas promoter (-109 to +20: p109). Different promoter constructs containing the SSE or middle region upstream of p109 or a CaMV 35S basal promoter (-64 to +6) were fused to gus. Each construct was expressed in seed, but not in vegetative tissues. Use of the various phas promoter regions yielded notable differences in relative GUS activity in embryo or endosperm. Addition of both the SSE and middle region resulted in higher activity than the sum of adding either element alone to p109, indicating synergistic interaction between these elements. Seeds from plants transformed with the proximal 227 bp of promoter (p227) showed embryo-specific GUS activity. In contrast, constructs containing two copies of the SSE element were preferentially expressed in the endosperm. These results illustrate the modular nature of the proximal phas promoter, where distinct elements contribute to high levels of expression in different parts of the seed.