RY repeats are conserved in the 5'-flanking regions of legume seed-protein genes

CRISPR/Cas9 Based Site-Specific Modification of FAD2 cis-Regulatory Motifs in Peanut (Arachis hypogaea L)

Peanut (Arachis hypogaea L.) seed is a rich source of edible oil, comprised primarily of monounsaturated oleic acid and polyunsaturated linoleic acid, accounting for 80% of its fatty acid repertoire. The conversion of oleic acid to linoleic acid, catalyzed by Fatty Acid Desaturase 2 (FAD2) enzymes, is an important regulatory point linked to improved abiotic stress responses while the ratio of these components is a significant determinant of commercial oil quality. Specifically, oleic acid has better oxidative stability leading to longer shelf life and better taste qualities while also providing nutritional based health benefits. Naturally occurring FAD2 gene knockouts that lead to high oleic acid levels improve oil quality at the potential expense of plant health though. We undertook a CRISPR/Cas9 based site-specific genome modification approach designed to downregulate the expression of two homeologous FAD2 genes in seed while maintaining regulation in other plant tissues. Two cis-regulatory elements the RY repeat motif and 2S seed protein motif in the 5′UTR and associated intron of FAD2 genes are potentially important for regulating seed-specific gene expression. Using hairy root and stable germ line transformation, differential editing efficiencies were observed at both CREs when targeted by single gRNAs using two different gRNA scaffolds. The editing efficiencies also differed when two gRNAs were expressed simultaneously. Additionally, stably transformed seed exhibited an increase in oleic acid levels relative to wild type. Taken together, the results demonstrate the immense potential of CRISPR/Cas9 based approaches to achieve high frequency targeted edits in regulatory sequences for the generation of novel transcriptional alleles, which may lead to fine tuning of gene expression and functional genomic studies in peanut.

Abscisic acid activation of oleosin gene HvOle3 expression prevents the coalescence of protein storage vacuoles in barley aleurone cells

Protein storage vacuoles (PSVs) in aleurone cells coalesce during germination, and this process is highly coupled with mobilization of PSV reserves, allowing de novo synthesis of various hydrolases in aleurone cells for endosperm degradation. Here we show that in barley (Hordeum vulgare L.) oleosins, the major integral proteins of oleosomes are encoded by four genes (HvOle1 to 4), and the expression of HvOle1 and HvOle3 is strongly up-regulated by abscisic acid (ABA), which shows antagonism to gibberellic acid. In aleurone cells, all HvOLEs were subcellularly targeted to the tonoplast of PSVs. Gain-of-function analyses revealed that HvOLE3 effectively delayed PSV coalescence, whereas HvOLE1 only had a moderate effect, with no notable effect of HvOLE2 and 4. With regard to longevity, HvOLE3 chiefly outperformed other HvOLEs, followed by HvOLE1. Experiments swapping the N- and C-terminal domain between HvOLE3 and other HvOLEs showed that the N-terminal region of HvOLE3 is mainly responsible, with some positive effect by the C-terminal region, for mediating the specific preventive effect of HvOLE3 on PSV coalescence. Three ACGT-core elements and the RY-motif were responsible for ABA induction of HvOle3 promoter activity. Transient expression assays using aleurone protoplasts demonstrated that transcriptional activation of the HvOle3 promoter was mediated by transcription factors HvABI3 and HvABI5, which acted downstream of protein kinase HvPKABA1.

Linkage and association study discovered loci and candidate genes for glycinin and β-conglycinin in soybean (Glycine max L. Merr.)

KEY MESSAGE

Linkage mapping and GWAS identified 67 QTLs related to soybean glycinin, β-conglycinin and relevant traits. Polymorphisms of the candidate gene Gy1 promoter were associated with the glycinin content in soybean. The major components of storage proteins in soybean seeds are glycinin and β-conglycinin, which play important roles in determining protein nutrition and soy food processing properties. Increasing the protein content while improving the ratio of glycinin to β-conglycinin is substantially important for soybean protein improvement. To investigate the genetic mechanism of storage protein subunits, 184 recombinant inbred lines (RILs) derived from a cross of Kefeng No. 1 and Nannong 1138-2 and 211 diverse soybean cultivars were used to detect loci related to glycinin (11S), β-conglycinin (7S), the sum of glycinin and β-conglycinin (SGC), and the ratio of glycinin to β-conglycinin (RGC). Sixty-seven QTLs and 11 hot genomic regions were identified as affecting the four traits. One genetic region (q10-1) on chromosome 10 was associated with multiple traits by both linkage and association analysis. Eight genes in 11 hot genomic regions might be related to soybean protein subunit. The candidate gene analysis showed that polymorphisms in Gy1 promoters were significantly correlated with the 11S content. The QTLs and candidate genes identified in the present study allow for further understanding the genetic basis of 11S and 7S regulation and provide useful information for marker-assisted selection (MAS) in soybean quality improvement.

Seed-specific activity of the Arabidopsis β-glucosidase 19 promoter in transgenic Arabidopsis and tobacco

KEY MESSAGE

The promoter of the Arabidopsis thaliana β-glucosidase 19 gene directs GUS expression in a seed-specific manner in transgenic Arabidopsis and tobacco. In the present study, an 898-bp putative promoter of the Arabidopsis β-glucosidase 19 (AtBGLU19) gene was cloned. The bioinformatics analysis of the cis-acting elements indicated that this putative promoter contains many seed-specific elements, such as RY elements. The features of this promoter fragment were evaluated for the capacity to direct the β-glucuronidase (GUS) reporter gene in transgenic Arabidopsis and tobacco. Histochemical and fluorometric GUS analyses of transgenic Arabidopsis plants revealed that the AtBGLU19 promoter directed strong GUS activity in late-maturing seeds and dry seeds, whereas no GUS expression was observed in other organs. The results indicated that the AtBGLU19 promoter was able to direct GUS expression in a seed-specific manner in transgenic Arabidopsis. In tobacco, the intensity of the staining and the level of GUS activity were considerably higher in the seeds than in the other tissues. These results further confirmed that the AtBGLU19 promoter is seed specific and can be used to control transgene expression in a heterologous plant system.

MADS78 and MADS79 Are Essential Regulators of Early Seed Development in Rice

MADS box transcription factors (TFs) are subdivided into type I and II based on phylogenetic analysis. The type II TFs regulate floral organ identity and flowering time, but type I TFs are relatively less characterized. Here, we report the functional characterization of two type I MADS box TFs in rice (Oryza sativa), MADS78 and MADS79 Transcript abundance of both these genes in developing seed peaked at 48 h after fertilization and was suppressed by 96 h after fertilization, corresponding to syncytial and cellularized stages of endosperm development, respectively. Seeds overexpressing MADS78 and MADS 79 exhibited delayed endosperm cellularization, while CRISPR-Cas9-mediated single knockout mutants showed precocious endosperm cellularization. MADS78 and MADS 79 were indispensable for seed development, as a double knockout mutant failed to make viable seeds. Both MADS78 and 79 interacted with MADS89, another type I MADS box, which enhances nuclear localization. The expression analysis of Fie1, a rice FERTILIZATION-INDEPENDENT SEED-POLYCOMB REPRESSOR COMPLEX2 component, in MADS78 and 79 mutants and vice versa established an antithetical relation, suggesting that Fie1 could be involved in negative regulation of MADS78 and MADS 79 Misregulation of MADS78 and MADS 79 perturbed auxin homeostasis and carbon metabolism, as evident by misregulation of genes involved in auxin transport and signaling as well as starch biosynthesis genes causing structural abnormalities in starch granules at maturity. Collectively, we show that MADS78 and MADS 79 are essential regulators of early seed developmental transition and impact both seed size and quality in rice.

Analyzing the action of evolutionarily conserved modules on HMW-GS 1Ax1 promoter activity

The specific and high-level expression of 1Ax1 is determined by different promoter regions. HMW-GS synthesis occurs in aleurone layer cells. Heterologous proteins can be stored in protein bodies. High-molecular-weight glutenin subunit (HMW-GS) is highly expressed in the endosperm of wheat and relative species, where their expression level and allelic variation affect the bread-making quality and nutrient quality of flour. However, the mechanism regulating HMW-GS expression remains elusive. In this study, we analyzed the distribution of cis-acting elements in the 2659-bp promoter region of the HMW-GS gene 1Ax1, which can be divided into five element-enriched regions. Fragments derived from progressive 5' deletions were used to drive GUS gene expression in transgenic wheat, which was confirmed in aleurone layer cells, inner starchy endosperm cells, starchy endosperm transfer cells, and aleurone transfer cells by histochemical staining. The promoter region ranging from - 297 to - 1 was responsible for tissue-specific expression, while fragments from - 1724 to - 618 and from - 618 to - 297 were responsible for high-level expression. Under the control of the 1Ax1 promoter, heterologous protein could be stored in the form of protein bodies in inner starchy endosperm cells, even without a special location signal. Our findings not only deepen our understanding of glutenin expression regulation, trafficking, and accumulation but also provide a strategy for the utilization of wheat endosperm as a bioreactor for the production of nutrients and metabolic products.

Identification of a seed maturation protein gene from Coffea arabica (CaSMP) and analysis of its promoter activity in tomato

A seed maturation protein gene (CaSMP) from Coffea arabica is expressed in the endosperm of yellow/green fruits. The CaSMP promoter drives reporter expression in the seeds of immature tomato fruits. In this report, an expressed sequence tag-based approach was used to identify a seed-specific candidate gene for promoter isolation in Coffea arabica. The tissue-specific expression of the cognate gene (CaSMP), which encodes a yet uncharacterized coffee seed maturation protein, was validated by RT-qPCR. Additional expression analysis during coffee fruit development revealed higher levels of CaSMP transcript accumulation in the yellow/green phenological stage. Moreover, CaSMP was preferentially expressed in the endosperm and was down-regulated during water imbibition of the seeds. The presence of regulatory cis-elements known to be involved in seed- and endosperm-specific expression was observed in the CaSMP 5'-upstream region amplified by genome walking (GW). Additional histochemical analysis of transgenic tomato (cv. Micro-Tom) lines harboring the GW-amplified fragment (~ 1.4 kb) fused to uidA reporter gene confirmed promoter activity in the ovule of immature tomato fruits, while no activity was observed in the seeds of ripening fruits and in the other organs/tissues examined. These results indicate that the CaSMP promoter can be used to drive transgene expression in coffee beans and tomato seeds, thus representing a promising biotechnological tool.

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.

Prediction and validation of cis-regulatory elements in 5' upstream regulatory regions of lectin receptor-like kinase gene family in rice

Lectin receptor-like kinases (LecRLKs) play crucial roles in regulating plant growth and developmental processes in response to stress. In transcriptional gene regulation for normal cellular functions, cis-acting regulatory elements (CREs) direct the temporal and spatial gene expression with respect to environmental stimuli. A complete insightful of the transcriptional gene regulation system relies on effective functional analysis of CREs. Here, we analyzed the potential putative CREs present in the promoters of rice LecRLKs genes by using PlantCARE database. The CREs in LecRLKs promoters are associated with plant growth/development, light response, plant hormonal regulation processes, various stress responses, hormonal response like ABA, root-specific expression responsive, drought responsive, and cell and organ specific regulatory elements. The effect of methylation on these cis-regulatory elements was also analyzed. Real-time analysis of rice seedling under various stress conditions showed the expression levels of selected LecRLK genes superimposing the number of different CREs present in 5' upstream region. The overall results showed that the possible CREs function in the selective expression/regulation of LecRLKs gene family and during rice plant development under stress.

Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed

In Arabidopsis (Arabidopsis thaliana), transcriptional control of seed maturation involves three related regulators with a B3 domain, namely LEAFY COTYLEDON2 (LEC2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (ABI3/FUS3/LEC2 [AFLs]). Although genetic analyses have demonstrated partially overlapping functions of these regulators, the underlying molecular mechanisms remained elusive. The results presented here confirmed that the three proteins bind RY DNA elements (with a 5'-CATG-3' core sequence) but with different specificities for flanking nucleotides. In planta as in the moss Physcomitrella patens protoplasts, the presence of RY-like (RYL) elements is necessary but not sufficient for the regulation of the OLEOSIN1 (OLE1) promoter by the B3 AFLs. G box-like domains, located in the vicinity of the RYL elements, also are required for proper activation of the promoter, suggesting that several proteins are involved. Consistent with this idea, LEC2 and ABI3 showed synergistic effects on the activation of the OLE1 promoter. What is more, LEC1 (a homolog of the NF-YB subunit of the CCAAT-binding complex) further enhanced the activation of this target promoter in the presence of LEC2 and ABI3. Finally, recombinant LEC1 and LEC2 proteins produced in Arabidopsis protoplasts could form a ternary complex with NF-YC2 in vitro, providing a molecular explanation for their functional interactions. Taken together, these results allow us to propose a molecular model for the transcriptional regulation of seed genes by the L-AFL proteins, based on the formation of regulatory multiprotein complexes between NF-YBs, which carry a specific aspartate-55 residue, and B3 transcription factors.

Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals

The legume-rhizobium symbiosis is initiated through the activation of the Nodulation (Nod) factor-signaling cascade, leading to a rapid reprogramming of host cell developmental pathways. In this work, we combine transcriptome sequencing with molecular genetics and network analysis to quantify and categorize the transcriptional changes occurring in roots of Medicago truncatula from minutes to days after inoculation with Sinorhizobium medicae. To identify the nature of the inductive and regulatory cues, we employed mutants with absent or decreased Nod factor sensitivities (i.e. Nodulation factor perception and Lysine motif domain-containing receptor-like kinase3, respectively) and an ethylene (ET)-insensitive, Nod factor-hypersensitive mutant (sickle). This unique data set encompasses nine time points, allowing observation of the symbiotic regulation of diverse biological processes with high temporal resolution. Among the many outputs of the study is the early Nod factor-induced, ET-regulated expression of ET signaling and biosynthesis genes. Coupled with the observation of massive transcriptional derepression in the ET-insensitive background, these results suggest that Nod factor signaling activates ET production to attenuate its own signal. Promoter:β-glucuronidase fusions report ET biosynthesis both in root hairs responding to rhizobium as well as in meristematic tissue during nodule organogenesis and growth, indicating that ET signaling functions at multiple developmental stages during symbiosis. In addition, we identified thousands of novel candidate genes undergoing Nod factor-dependent, ET-regulated expression. We leveraged the power of this large data set to model Nod factor- and ET-regulated signaling networks using MERLIN, a regulatory network inference algorithm. These analyses predict key nodes regulating the biological process impacted by Nod factor perception. We have made these results available to the research community through a searchable online resource.

Isolation and sequence analysis of napin seed specific promoter from Iranian Rapeseed (Brassica napus L.)

Rapeseed (Brassica napus L.) has become an important crop during the last 30years. In addition to a high lipid level, the seeds also have a significant protein content, which constitutes 20-25% of the dry seed weight. The synthesis of storage proteins is primarily controlled at transcriptional level and seed-specific expression has been shown to be conferred upon the promoter regions of many storage protein genes. Napin is one of the main storage proteins in rapeseed(')s embryo that is produced in seed developing stage. Its promoter region located at 5' upstream of the napin gene has already been isolated (GenBank number, EU416279.1). In current research, seed-specific promoter (napin) of Iranian B. napus L. was isolated from the genomic DNA and cloned into pBI121 plant binary vector to use in future researches. For this purpose, the napin promoter was amplified by PCR method using specific primers, cloned in pSK(+) vector and sequenced. Sequencing analysis showed that the cloned promoter contained all of conserved motifs such as TATA box (TATAAA), RY repeats (CATGCA), dist-B (TCAAACACC) and prox-B elements (GCCACTTGTC), G-box (CACGTG) and CAAT Motifs, which constituted the seed-specific promoter activity and according to this analysis, the seed-specific promoter activity of cloned sequence was predicted. Based on sequence distances of nucleotide sequences, our sequence had the highest similarity (99.8%) whit B. napus sequence (with EU416279.1 accession number). Finally the promoter obtained might be interesting not only as a useful tool for biotechnological application but also for fundamental research.

Structural and functional analysis of various globulin proteins from soy seed

Storage proteins of soybean mostly consist of globulins, which are classified according to their sedimentation coefficient. Among 4 major types: 2S, 7S, 11S, and 15S of globulins, 7S and 11S constitute major fraction. The 11S fraction consists only of glycinin and 7S fraction majorly consists of β-conglycinin, small amounts of γ-conglycinin and basic 7S globulin (Bg7S). Glycinin exist as a hexamer while β-conglycinin as a trimer and Bg7S as a tetramer. Glycinin subunits are coded by 5 genes of a family, whereas about 15 genes are present for β-conglycinin subunits. Bg7S gene is present in four copies in soybean genome. Synthesis of all proteins takes place as a single polypeptide chain, which is cleaved after folding to yield different chains or subunits. Glycinin and β-Conglycinin are made for storage purpose. However, Bg7S has potential xylanase inhibition activity and protein kinase activity. Primary structure of Bg7S reveals 12 conserved cysteine residues involved in forming 6 disulfide bonds, which provides appreciable stability to protein. Secondary structure is predominately rich in β-sheets with few alpha helices. Bg7S shares structural similarity with various aspartic-proteases. In this review, our aim is to discuss sequence, structure, and function of various globulins present in Glycine max.

Profiles of embryonic nuclear protein binding to the proximal promoter region of the soybean β-conglycinin α subunit gene

β-Conglycinin, a major component of seed storage protein in soybean, comprises three subunits: α, α' and β. The expression of genes for these subunits is strictly controlled during embryogenesis. The proximal promoter region up to 245 bp upstream of the transcription start site of the α subunit gene sufficiently confers spatial and temporal control of transcription in embryos. Here, the binding profile of nuclear proteins in the proximal promoter region of the α subunit gene was analysed. DNase I footprinting analysis indicated binding of proteins to the RY element and DNA regions including box I, a region conserved in cognate gene promoters. An electrophoretic mobility shift assay (EMSA) using different portions of box I as a probe revealed that multiple portions of box I bind to nuclear proteins. In addition, an EMSA using nuclear proteins extracted from embryos at different developmental stages indicated that the levels of major DNA-protein complexes on box I increased during embryo maturation. These results are consistent with the notion that box I is important for the transcriptional control of seed storage protein genes. Furthermore, the present data suggest that nuclear proteins bind to novel motifs in box I including 5'-TCAATT-3' rather than to predicted cis-regulatory elements.

Isolation and functional characterization of a novel seed-specific promoter region from peanut

The importance of using tissue-specific promoters in the genetic transformation of plants has been emphasized increasingly. Here, we report the isolation of a novel seed-specific promoter region from peanut and its validation in Arabidopsis and tobacco seeds. The reported promoter region referred to as groundnut seed promoter (GSP) confers seed-specific expression in heterologous systems, which include putative promoter regions of the peanut (Arachis hypogaea L.) gene 8A4R19G1. This region was isolated, sequenced, and characterized using gel shift assays. Tobacco transgenics obtained using binary vectors carrying uidA reporter gene driven by GSP and/or cauliflower mosaic virus 35S promoters were confirmed through polymerase chain reaction (PCR), RT-PCR, and computational analysis of motifs which revealed the presence of TATA, CAAT boxes, and ATG signals. This seed-specific promoter region successfully targeted the reporter uidA gene to seed tissues in both Arabidopsis and tobacco model systems, where its expression was confirmed by histochemical analysis of the transgenic seeds. This promoter region is routinely being used in the genetic engineering studies in legumes aimed at targeting novel transgenes to the seeds, especially those involved in micronutrient enhancement, fungal resistance, and molecular pharming.

Genome-wide analysis of endosperm-specific genes in rice

The endosperm of the cereal crop is an important nutrient source for humans. It also acts as a critical integrator of plant seed growth and development. Despite its importance, the comprehensive understanding in regulating of endosperm development in rice remains elusive. Here, we performed a genomic survey comprising the identification and functional characterization of the endosperm-specific genes (OsEnS) in rice using Affymetrix microarray data and Gene Ontology (GO) analysis. A total of 151 endosperm-specific genes were identified, and the expression patterns of 13 selected genes were confirmed by qRT-PCR analysis. Promoter regions of the endosperm-specific expression genes were analyzed by PLACE Signal Scan Search. The results indicated that some motifs were involved in endosperm-specific expression regulation, and some cis-elements were responsible for hormone regulation. The bootstrap analysis indicated that the RY repeat (CATGCA box) was over-represented in promoter regions of endosperm-specific expression genes. GO analysis indicated that these genes could be classified into 12 groups, namely, transcription factor, stress/defense, seed storage protein (SSP), carbohydrate and energy metabolism, seed maturation, protein metabolism, lipid metabolism, transport, cell wall related, hormone related, signal transduction, and one unclassified group. Taken together, our results provide informative clues for further functional characterization of the endosperm-specific genes, which facilitate the understanding of the molecular mechanism in rice endosperm development.

DISPOM: A DISCRIMINATIVE DE-NOVO MOTIF DISCOVERY TOOL BASED ON THE JSTACS LIBRARY

DNA-binding proteins are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in target regions of genomic DNA. However, de-novo discovery of these binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not yet been solved satisfactorily.

Here, we present a detailed description and analysis of the de-novo motif discovery tool Dispom, which has been developed for finding binding sites of DNA-binding proteins that are differentially abundant in a set of target regions compared to a set of control regions. Two additional features of Dispom are its capability of modeling positional preferences of binding sites and adjusting the length of the motif in the learning process.

Dispom yields an increased prediction accuracy compared to existing tools for de-novo motif discovery, suggesting that the combination of searching for differentially abundant motifs, inferring their positional distributions, and adjusting the motif lengths is beneficial for de-novo motif discovery. When applying Dispom to promoters of auxin-responsive genes and those of ABI3 target genes from Arabidopsis thaliana, we identify relevant binding motifs with pronounced positional distributions. These results suggest that learning motifs, their positional distributions, and their lengths by a discriminative learning principle may aid motif discovery from ChIP-chip and gene expression data.

We make Dispom freely available as part of Jstacs, an open-source Java library that is tailored to statistical sequence analysis. To facilitate extensions of Dispom, we describe its implementation using Jstacs in this manuscript. In addition, we provide a stand-alone application of Dispom at http://www.jstacs.de/index.php/Dispom for instant use.

Cellular localization of the embryo-specific hybrid PRP from Zea mays, and characterization of promoter regulatory elements of its gene

The expression, regulation and cellular localization of ZmHyPRP, a gene marker of embryo differentiation whose expression declines after ABA induction, was studied. ZmHyPRP is a proline-rich protein with a C-terminal domain having eight cysteines in a CM8 pattern. Transient expression in onion epidermal cells, transformed with a 2x35S::ZmHyPRP-GFP construction, indicated the protein is present in vesicles lining the membrane of the cell. The ZmHyPRP gene expression is under the control of classic promoter seed-specific regulatory elements such as Sph/RY and G-boxes, suggesting regulation by B3 and b-ZIP transcription factors. Promoter deletion analysis, by particle-bombardment transient transformation of maize immature embryos with serial deletions of the promoter fused to GUS, showed the presence of two negative regulatory elements, NE1 (-2070 to -1280) and NE2 (-232 to -178), in the ZmHyPRP promoter. By selective deletion or mutation of ZmHyPRP regulatory promoter elements we conclude that the promoter expression is attenuated by the NE2 element as well as by the G-box2 and the Sph1-2 box together with the G-box2.

Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription

BACKGROUND

In higher plants, a diverse array of developmental and growth-related processes is regulated by the plant hormone auxin. Recent publications have proposed that besides the well-characterized Auxin Response Factors (ARFs) that bind Auxin Response Elements (AuxREs), also members of the bZIP- and MYB-transcription factor (TF) families participate in transcriptional control of auxin-regulated genes via bZIP Response Elements (ZREs) or Myb Response Elements (MREs), respectively.

RESULTS

Applying a novel bioinformatic algorithm, we demonstrate on a genome-wide scale that singular motifs or composite modules of AuxREs, ZREs, MREs but also of MYC2 related elements are significantly enriched in promoters of auxin-inducible genes. Despite considerable, species-specific differences in the genome structure in terms of the GC content, this enrichment is generally conserved in dicot (Arabidopsis thaliana) and monocot (Oryza sativa) model plants. Moreover, an enrichment of defined composite modules has been observed in selected auxin-related gene families. Consistently, a bipartite module, which encompasses a bZIP-associated G-box Related Element (GRE) and an AuxRE motif, has been found to be highly enriched. Making use of transient reporter studies in protoplasts, these findings were experimentally confirmed, demonstrating that GREs functionally interact with AuxREs in regulating auxin-mediated transcription.

CONCLUSIONS

Using genome-wide bioinformatic analyses, evolutionary conserved motifs have been defined which potentially function as AuxRE-dependent coupling elements to establish auxin-specific expression patterns. Based on these findings, experimental approaches can be designed to broaden our understanding of combinatorial, auxin-controlled gene regulation.

Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon

The plant-specific, B3 domain-containing transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) is an essential component of the regulatory network controlling the development and maturation of the Arabidopsis thaliana seed. Genome-wide chromatin immunoprecipitation (ChIP-chip), transcriptome analysis, quantitative reverse transcriptase–polymerase chain reaction and a transient promoter activation assay have been combined to identify a set of 98 ABI3 target genes. Most of these presumptive ABI3 targets require the presence of abscisic acid for their activation and are specifically expressed during seed maturation. ABI3 target promoters are enriched for G-box-like and RY-like elements. The general occurrence of these cis motifs in non-ABI3 target promoters suggests the existence of as yet unidentified regulatory signals, some of which may be associated with epigenetic control. Several members of the ABI3 regulon are also regulated by other transcription factors, including the seed-specific, B3 domain-containing FUS3 and LEC2. The data strengthen and extend the notion that ABI3 is essential for the protection of embryonic structures from desiccation and raise pertinent questions regarding the specificity of promoter recognition.

Genome change in wheat observed through the structure and expression of α/β-gliadin genes

To better understand genome structure and the expression of α/β-gliadin multigenes in hexaploid wheat, bacterial artificial chromosome (BAC) clones containing α/β-gliadin genes from the three loci, Gli-A2, Gli-B2, and Gli-D2, were screened. Based on their restriction fragment patterns, we selected five BAC clones, namely, two clones for Gli-A2, two clones for Gli-B2, and one clone for Gli-D2, to fully sequence. Approximately 200 kb was sequenced for each locus. In total, twelve α/β-gliadin intact genes and four pseudogenes were found, and retrotransposons or other transposons existed in each BAC clone. Dot-plot analysis revealed the pattern of genome segmental duplication within each BAC. We calculated time since duplication of each set of α/β-gliadin genes and insertion of retrotransposons. Duplication of all adjacent genes within the same BAC clone took place before or after allotetrapolyploidization, but duplication of certain genes occurred before diploid differentiation of wheat species. Retrotransposons were also inserted before and after the segmental duplication events. Furthermore, translocation of α/β-gliadin genes from chromosomes 1 to 6 apparently occurred before the diversification of various wheat genomes. Duplication of genome segments containing α/β-gliadin genes and retrotransposons were brought about through unequal crossing-over or saltatory replication and α/β-gliadin genes per se were duplicated without any recombination events. Out of twelve intact α/β-gliadin genes detected from their sequences, nine were expressed, although their patterns of expression were distinct. Since they have similar cis-elements and promoter structures, the mechanisms underlying their distinct gene expression and possible applications are discussed.

Reporter Gene Expression Patterns Regulated by an Ara h 2 Promoter Differ in Homologous Versus Heterologous Systems1

Peanut (Arachis hypogaea L.) is a globally important crop whose seeds are widely used in food products. Peanut seeds contain proteins that serve a nutrient reservoir function and that also are major allergens. As part of an investigation to determine the effect of reducing/eliminating the peanut allergen Ara h 2 from seeds, gene sequence including upstream regulatory regions was characterized. The ability of regions upstream of the translation initiation site to regulate seed-specific expression of reporter genes was tested in peanut and Arabidopsis. Two independent transgenic peanut lines biolistically transformed with 1kb of DNA upstream of the Ara h 2.02 (B-genome) coding sequence controlling a Green Fluorescent Protein – β-glucuronidase (Gfp-Gus) fusion were obtained. All T1, T2 and T3 generations of transgenic plants showed the expression of GFP and GUS restricted to seeds and near background levels in vegetative tissues. However, constitutive GUS expression was observed in Arabidopsis transgenic lines, a heterologous system. It is possible that trans-acting factors regulating seed specificity in peanut are too divergent in Arabidopsis to enable the seed specific response. Thus, the promoter described in this paper may have potential use for expression of transgenes in peanut where seed-specificity is desired, but expression patterns should be tested in heterologous systems prior to off-the-shelf adoption.

Regulation of the ABA-responsive Em promoter by ABI3 in the moss Physcomitrella patens: role of the ABA response element and the RY element

The plant-specific transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) or the maize ortholog VIVIPAROUS1 (VP1) is known to regulate seed maturation and germination in concert with the phytohormone abscisic acid (ABA) but is also evolutionarily conserved among land plants including non-seed plants. An ABI3/VP1 ortholog (PpABI3A) from the moss Physcomitrella patens can activate ABA-responsive gene promoters in the moss and angiosperms; however, it failed to fully complement the phenotypes of the Arabidopsis abi3-6 mutant, suggesting that some aspects of ABI3/VP1 functions have diverged during the evolution of land plants. To gain insights into the evolution of ABI3/VP1 function, we performed a comparative analysis of the regulatory elements required for ABI3 activation in Physcomitrella using a wheat Em gene promoter, which is induced by ABA and ABI3/VP1 both in Physcomitrella and in angiosperms. Elimination of either the ACGT core motif in the ABA response element (ABRE) or the RY element, to which ABI3/VP1 binds directly, resulted in a drastic reduction of the ABA response in Physcomitrella. Arabidopsis ABI3 could effectively activate the Em promoter either in an ABRE- or RY-dependent manner, as observed in angiosperms. On the other hand, PpABI3A failed to activate an Em promoter lacking the RY element but not the ABRE. These results suggest that RY-mediated transcriptional regulation of ABI3/VP1 is evolutionarily conserved between the moss and angiosperms, whereas angiosperm ABI3/VP1 has evolved to activate ABA-inducible promoters via the ABRE sequence independently from the RY element.

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

BACKGROUND

Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs.

RESULTS

We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins.

CONCLUSION

Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs. The majority of discovered motifs match experimentally characterized cis-regulatory elements. These results provide a good starting point for further experimental analysis of plant seed-specific promoters and our methodology can be used to unravel more transcriptional regulatory mechanisms in plants and other eukaryotes.

Efficient LEC2 activation of OLEOSIN expression requires two neighboring RY elements on its promoter

As the main structural protein of oil body, OLEOSIN is highly expressed only during seed development. OLEOSIN promoter is a very useful tool for seed-specific gene engineering and seed bioreactor designing. The B3 domain transcription factor leafy cotyledon2 (LEC2) plays an important role in regulating seed development and seed-specific gene expression. Here, we first report how seed-specific B3 domain transcription factor leafy cotyledon2 (LEC2) efficiently activates OLEOSIN expression. The central promoter region of OLEOSIN, responsible for seed specificity and LEC2 activation, was determined by 5'-deletion analysis. Binding experiments in yeast cells and electrophoretic mobility shift assays showed that LEC2 specifically bound to two conserved RY elements in this region. In transient expression assays, mutation in either RY element dramatically reduced LEC2 activation of OLEOSIN promoter activity, while double mutation abolished it. Analysis of the distribution of RY elements in seed-specific genes activated by LEC2 also supported the idea that genes containing neighboring RY elements responded strongly to LEC2 activation. Therefore, we conclude that two neighboring RY elements are essential for efficient LEC2 activation of OLEOSIN expression. These findings will help us better utilize seed-specific promoter activity.

Developmental and environmental regulation of soybean SE60 gene expression during embryogenesis and germination

Soybean SE60 belongs to the gamma-thionin family of proteins. We recently demonstrated that SE60 plays a role in defense during soybean development. Here, we show that SE60 is expressed in a tissue-specific and developmentally regulated manner. The expression of SE60 is distinct from that of the glycinin (Gy2) and extensin (SbHRGP3) genes of soybean during embryogenesis and germination. A SE60::GUS(-809) transgene, comprising -809 bp of the 5'-flanking region of SE60 fused to the GUS reporter gene, was expressed specifically in developing embryos, but not in the endosperms, from the globular stage of transgenic tobacco and Arabidopsis seeds. Furthermore, light affected the SE60::GUS(-809) expression pattern in germinating seedlings. Electrophoretic mobility shift assay (EMSA) revealed that soybean nuclear proteins as well as E. coli-expressed SB16, a high mobility group protein (HMG), were bound sequence-specifically to the fragment containing AT-rich motifs identified in the SE60 promoter. Interestingly, the soybean nuclear proteins binding to the two G-boxes and RY repeat were prevalent in seeds of 2-4 mm in size. In contrast, the nuclear proteins binding to the AT-rich motif and SE60 RNA expression were more prominent in seeds of 4-6 mm in size. Therefore, we propose that factors binding to the G-boxes or RY repeat initiate SE60 expression during embryogenesis.

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.

Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis

Seeds represent the main source of nutrients for animals and humans, and knowledge of their biology provides tools for improving agricultural practices and managing genetic resources. There is also tremendous interest in using seeds as a sustainable alternative to fossil reserves for green chemistry. Seeds accumulate large amounts of storage compounds such as carbohydrates, proteins and oils. It would be useful for agro-industrial purposes to produce seeds that accumulate these storage compounds more specifically and at higher levels. The main metabolic pathways necessary for oil, starch or protein accumulation are well characterized. However, the overall regulation of partitioning between the various pathways remains unclear. Such knowledge could provide new molecular tools for improving the qualities of crop seeds (Focks and Benning, 1998, Plant Physiol. 118, 91). Studies to improve understanding of the genetic controls of seed development and metabolism therefore remain a key area of research. In the model plant Arabidopsis, genetic analyses have demonstrated that LEAFY COTYLEDON genes, namely LEC1, LEC2 and FUSCA3 (FUS3), are key transcriptional regulators of seed maturation, together with ABSCISIC ACID INSENSITIVE 3 (ABI3). Interestingly, LEC2, FUS3 and ABI3 are related proteins that all contain a 'B3' DNA-binding domain. In recent years, genetic and molecular studies have shed new light on the intricate regulatory network involving these regulators and their interactions with other factors such as LEC1, PICKLE, ABI5 or WRI1, as well as with sugar and hormonal signaling. Here, we summarize the most recent advances in our understanding of this complex regulatory network and its role in the control of seed maturation.

Combinatorial interactions of multiple cis-elements regulating the induction of the Arabidopsis XERO2 dehydrin gene by abscisic acid and cold

Multiple combinations of mutations in the promoter of the XERO2 dehydrin gene were used to identify elements involved in ABA and cold induction. Mutating one of the three ACGT elements (ACGT1) increases expression in the absence of cold or ABA. An AT-rich element is a novel partner (coupling element) of ACGT-containing ABA-responsive cis-elements. A 12-bp palindrome also acts as a coupling element for ABA induction and includes one of the three dehydration-responsive element/C-repeat (DRE/CRT) elements and two overlapping motifs (TGTCG and TCGGC) previously shown to be statistically enriched in ABA-dependent and 'VP1 or ABA'-dependent activated genes (Plant Physiol. 2005; 139:437). At least two of the DRE/CRT elements are required for significant cold induction. During cold induction the AT-rich element also functions as a coupling element and ACGT1 is involved in repressing this induction. Two of the ACGT and DRE/CRT elements overlap, and mutating a single base in the ACGT of either of the two GCCGACGT sequences while retaining a DRE element reduced both ABA and cold induction. Changing the spatial relationships between the elements by deletion, inversion or insertion of DNA sequences reduced both cold and ABA induction. Overexpression of CBF1, -2 or -3 induced XERO2 expression in untreated plants. The ABI5 transcription factor may have a role in ABA-induced XERO2 expression, whereas ABI3 and ABI4 do not. The GCA2 gene was essential for both cold and ABA induction. A combination of the same overlapping and shared elements is used in the regulation of transcription by ABA and cold.

Dissection of a complex seed phenotype: novel insights of FUSCA3 regulated developmental processes

A T-DNA insertion mutant of FUSCA3 (fus3-T) in Arabidopsis thaliana exhibits several of the expected deleterious effects on seed development, but not the formation of brown seeds, a colouration which results from the accumulation of large amounts of anthocyanin. A detailed phenotypic comparison between fus3-T and a known splice point mutant (fus3-3) revealed that the seeds from both mutants do not enter dormancy and can be rescued at an immature stage. Without rescue, mature fus3-3 seeds are non-viable, whereas those of fus3-T suffer only a slight loss in their germinability. A series of comparisons between the two mutants uncovered differences with respect to conditional lethality, in histological and sub-cellular features, and in the relative amounts of various storage compounds and metabolites present, leading to a further dissection of developmental processes in seeds and a partial reinterpretation of the complex seed phenotype. FUS3 function is now known to be restricted to the acquisition of embryo-dependent seed dormancy, the determination of cotyledonary cell identity, and the synthesis and accumulation of storage compounds. Based on DNA binding studies, a model is presented which can explain the differences between the mutant alleles. The fus3-T lesion is responsible for loss of function only, while the fus3-3 mutation induces various pleiotropic effects conditioned by a truncation gene product causing severe mis-differentiation.

Phylogenetic footprints in fern spore- and seed-specific gene promoters

Spermatophyte seed-storage proteins have descended from a group of proteins involved in cellular desiccation/hydration processes. Conserved protein structures are found across all plant phyla and in the fungi and Archaea. We investigated whether conservation in the coding region sequence is paralleled by common gene regulatory processes. Seed- and spore-specific gene promoters of three phylogenetically diverse plants were analysed by transient and transgenic expression in Arabidopsis thaliana and tobacco. The transcription factors FUS3 and ABI3, which are central regulators of seed maturation processes, interact with cis-motifs of seed-specific promoters from distantly related plants. The promoter of a fern spore-specific gene encoding a seed-storage globulin-like protein exhibits strong seed-specific activity in both Arabidopsis and tobacco. The existence of phylogenetic footprints indicates good conservation of regulatory pathways controlling gene expression in fern spores and in gymnosperm and angiosperm seeds, reflecting the concerted evolution of coding and regulatory regions.

Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination

The transition between dormancy and germination represents a critical stage in the life cycle of higher plants and is an important ecological and commercial trait. In this review we present current knowledge of the molecular control of this trait in Arabidopsis thaliana, focussing on important components functioning during the developmental phases of seed maturation, after-ripening and imbibition. Establishment of dormancy during seed maturation is regulated by networks of transcription factors with overlapping and discrete functions. Following desiccation, after-ripening determines germination potential and, surprisingly, recent observations suggest that transcriptional and post-transcriptional processes occur in the dry seed. The single-cell endosperm layer that surrounds the embryo plays a crucial role in the maintenance of dormancy, and transcriptomics approaches are beginning to uncover endosperm-specific genes and processes. Molecular genetic approaches have provided many new components of hormone signalling pathways, but also indicate the importance of hormone-independent pathways and of natural variation in key regulatory loci. The influence of environmental signals (particularly light) following after-ripening, and the effect of moist chilling (stratification) are increasingly being understood at the molecular level. Combined postgenomics, physiology and molecular genetics approaches are beginning to provide an unparalleled understanding of the molecular processes underlying dormancy and germination.

GASA4, one of the 14-member Arabidopsis GASA family of small polypeptides, regulates flowering and seed development

Members of the plant-specific gibberellic acid-stimulated Arabidopsis (GASA) gene family play roles in hormone response, defense and development. We have identified six new Arabidopsis GASA genes, bringing the total number of family members to 14. Here we show that these genes all encode small polypeptides that share the common structural features of an N-terminal putative signal sequence, a highly divergent intermediate region and a conserved 60 amino acid C-terminal domain containing 12 conserved cysteine residues. Analysis of promoter::GUS (beta-glucuronidase) transgenic plants representing six different GASA loci reveals that the promoters are activated in a variety of stage- and tissue-specific patterns during development, indicating that the GASA genes are involved in diverse processes. Characterization of GASA4 shows that the promoter is active in the shoot apex region, developing flowers and developing embryos. Phenotypic analyses of GASA4 loss-of-function and gain-of-function lines indicate that GASA4 regulates floral meristem identity and also positively affects both seed size and total seed yield.

The regulatory function of the upstream sequence of the beta-conglycinin alpha subunit gene in seed-specific transcription is associated with the presence of the RY sequence

beta-conglycinin, a major component of seed-storage proteins in soybean, comprises three subunits: alpha, alpha', and beta. Expression of these genes is spatially regulated in a stringent manner and occurs during seed development. To understand the mechanisms that control expression of the alpha subunit gene, we analyzed the nucleotide sequence of the 2.9-kb region upstream of the gene. The upstream sequence up to -1357 or a series of its 5'-deleted derivatives was fused to the beta-glucuronidase (GUS) gene. These reporter gene constructs were introduced into Arabidopsis thaliana plants via Agrobacterium-mediated gene transfer. Prominent GUS activity was detected in developing seeds of the T3 generation when 245 bp or longer sequences of the upstream region were fused to the GUS gene. We found a clear association of decreased GUS activity with a stepwise deletion of a region containing the RY sequence from the original construct. These results are consistent with the notion that multiple sequence elements including the RY sequences are involved in the seed-specific transcriptional activation of the beta-conglycinin alpha subunit gene in soybean.

Oleosin gene family of Coffea canephora: quantitative expression analysis of five oleosin genes in developing and germinating coffee grain

Coffee grains have an oil content between 10% and 16%, with these values associated with Coffea canephora (robusta) and C. arabica (arabica), respectively. As the majority of the oil stored in oil seeds is contained in specific structures called oil bodies, we were interested in determining whether there are any differences in the expression of the main oil body proteins, the oleosins, between the robusta and arabica varieties. Here, we present the isolation, characterization and quantitative expression analysis of six cDNAs representing five genes of the coffee oleosin family (CcOLE-1 to CcOLE-5) and one gene of the steroleosin family (CcSTO-1). Each coffee oleosin cDNA encodes for the signature structure for oleosins, a long hydrophobic central sequence containing a proline KNOT motif. Sequence analysis also indicates that the C-terminal domain of CcOLE-1, CcOLE-3 and CcOLE-5 contain an 18-residue sequence typical of H-form oleosins. Quantitative RT-PCR showed that the transcripts of all five oleosins were predominantly expressed during grain maturation in robusta and arabica grain, with CcOLE-1 and CcOLE-2 being more highly expressed. While the relative expression levels of the five oleosins were similar for robusta and arabica, significant differences in the absolute levels of expression were found between the two species. Quantitative analysis of oleosin transcripts in germinating arabica grain generally showed that the levels of these transcripts were lower in the grain after drying, and then further decreased during germination, except for a small spike of expression for CcOLE-2 early in germination. In contrast, the levels of CcSTO-1 transcripts remained relatively constant during germination, in agreement with suggestions that this protein is actively involved in the process of oil body turnover. Finally, we discuss the implications of the coffee oleosin expression data presented relative to the predicted roles for the different coffee oleosins during development and germination.

Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis

The B3 domain protein LEAFY COTYLEDON2 (LEC2) is required for several aspects of embryogenesis, including the maturation phase, and is sufficient to induce somatic embryo development in vegetative cells. Here, we demonstrate that LEC2 directly controls a transcriptional program involved in the maturation phase of seed development. Induction of LEC2 activity in seedlings causes rapid accumulation of RNAs normally present primarily during the maturation phase. Several RNAs encode proteins with known roles in maturation processes, including seed-storage and lipid-body proteins. Clustering analyses identified other LEC2-induced RNAs not previously shown to be involved in the maturation phase. We show further that genes encoding these maturation RNAs all possess in their 5' flanking regions RY motifs, DNA elements bound by other closely related B3 domain transcription factors. Our finding that recombinant LEC2 specifically binds RY motifs from the 5' flanking regions of LEC2-induced genes provides strong evidence that these genes represent transcriptional targets of LEC2. Although these LEC2-induced RNAs accumulate primarily during the maturation phase, we show that a subset, including AGL15 and IAA30, accumulate in seeds containing zygotes. We discuss how identification of LEC2 target genes provides a potential link between the roles of LEC2 in the maturation phase and in the induction of somatic embryogenesis.

Isolation and computer analysis of the 5'-regulatory region of the seed storage protein gene from buckwheat (Fagopyrum esculentum Moench)

Using the modified rapid amplification of cDNA ends (5'-RACE) approach, a fragment containing the 955 bp long 5'-regulatory region of the buckwheat storage globulin gene (FeLEG1) has been amplified from the genomic DNA of buckwheat. The entire fragment was sequenced, and the sequence was analyzed by computer prediction of cis-regulatory elements possibly involved in tissue-specific and developmentally controlled seed storage protein gene expression. The promoter obtained might be interesting not only for fundamental research but also as a useful tool for biotechnological application.

Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed

To reveal the transcriptomes of Arabidopsis seed, comprehensive expression analysis was performed using ATH1 GeneChips (Affymetrix, Santa Clara, CA, USA). In the dry seed, more than 12 000 stored mRNA species were detected, including all ontological categories. Statistical analysis revealed that promoters of highly expressed genes in wild-type dry seeds overrepresented abscisic acid-responsive elements (ABREs) containing the core motif ACGT. Although the coupling element and seed-specific enhancer RY motif alone were not prominently overrepresented in genes with high expression, the presence of these elements in combination with ABRE was associated with particularly high gene expression. The transcriptome of the imbibed seeds differed from that of the dry seed even at 6 h after seed imbibition. After imbibition many upregulated and downregulated genes were co-regulated in clusters of three to five genes. Genes for which expression was affected by the abi5 mutation tended to be located in clusters, suggesting that transactivation by ABI5 is not restricted to a single gene, but affects other proximal genes. Furthermore, cytosine methylation was observed not only in large silent retrotransposon clusters in centromeric regions, but also in non-centromeric silent gene clusters in the seed. These results suggest that such regions might be transcriptionally silenced by methylation or heterochromatin structures. Our analyses reveal that transcriptomes of Arabidopsis seed are characterized by multiple regulatory mechanisms: epigenetic chromatin structures, chromosomal locations (e.g. co-regulated gene clusters) and cis-acting elements.

Indirect ABA-dependent regulation of seed storage protein genes by FUSCA3 transcription factor in Arabidopsis

The key transcription factors that control seed maturation, ABSCISIC ACID INSENSITIVE3 (ABI3) and FUSCA3 (FUS3), share homologous DNA-binding domains. Regulation of seed storage protein genes At2S3 and CRC by ABI3 and FUS3 was investigated using transgenic plants in which ABI3 and FUS3 could be ectopically induced by steroid hormones. Like ABI3, the presence of FUS3 led to expression of At2S3 and CRC in vegetative tissues. FUS3-mediated induction of CRC was completely dependent on exogenous abscisic acid (ABA), while At2S3 was weakly induced without ABA but strongly enhanced with ABA. This ABA dependency of FUS3-induced CRC and At2S3 expression was similar to that observed for ABI3. However, kinetic analysis revealed distinctions between the mechanisms of ABA-dependent CRC regulation by FUS3 or ABI3, and between target genes. While At2S3 activation by FUS3 was rapid, CRC induction by FUS3 in the presence of ABA, and by ABA followed by the presence of FUS3, took a significantly longer time (24-36 h). This suggested the involvement of an indirect mechanism requiring the ABA- and FUS3-dependent synthesis of intermediate regulatory factor(s). A chimeric protein composed of the FUS3 B3 domain, and a heterologous activation domain and nuclear localization signal exhibited a tight coupling with ABA regulation as observed for wild-type FUS3. Simultaneous induction of FUS3 and ABI3 did not result in the synergistic activation of CRC and At2S3. Based on these results, similarities and differences in the mechanisms of seed storage protein gene regulation by FUS3 and ABI3 are discussed.

Seed-specific transcription factors ABI3 and FUS3: molecular interaction with DNA

In Arabidopsis thaliana (L.) Heynh. the seed-specific transcription factors ABI3 and FUS3 have key regulatory functions during the development of mature seeds. The highly conserved RY motif [DNA motif CATGCA(TG)], present in many seed-specific promoters, is an essential target of both regulators. Here we show that, in vitro, the full-length ABI3 protein, as well as FUS3 protein, is able to bind to RY-DNA and that the B3 domains of both transcription factors are necessary and sufficient for the specific interaction with the RY element. Flanking sequences of the RY motif modulate the binding, but the presence of an RY sequence alone allows the specific interaction of ABI3 and FUS3 with the target in vitro. Transcriptional activity of ABI3 and FUS3, measured by transient promoter activation, requires the B3 DNA-binding domain and an activation domain. In addition to the known N-terminal-located activation domain, a second transcription activation domain was found in the B1 region of ABI3.

ABI3 mediates expression of the peroxiredoxin antioxidant AtPER1 gene and induction by oxidative stress

The peroxiredoxin antioxidant gene AtPER1 has been considered to be specifically expressed in the embryo and aleurone layer during maturation and desiccation stages of development, and in the mature seed, typically for late embryogenesis-abundant (lea) transcripts. In the abscisic acid-insensitive abi3-1 mutant, the AtPER1 transcript level is strongly reduced, suggesting ABI3 to be a prime regulator of AtPER1. We have studied the expression pattern and regulation of AtPER1 with a series of nine promoter::GUS constructs with deletions and/or mutations in putative regulatory elements. Arabidopsis lines harbouring these constructs revealed AtPER1 promoter activity in the endosperm, especially the chalazal cyst, already when the embryo is in the late globular stage, in the embryo from the late torpedo stage, and in distinct cells of unfertilized and fertilized ovules. Early expression seems to be dependent on a putative antioxidant-responsive promoter element (ARE), while from the bent cotyledon stage endosperm and embryo expression is dependent on an ABA-responsive element (ABRE) likely to bind ABI5. The shortest promoter fragment (113 bp), devoid of ARE, ABRE and without an intact RY/Sph element thought to bind ABI3 did not drive GUS expression. The AtPER1::GUS construct also revealed expression in cotyledons, meristems and stem branching points. In general, seed and vegetative expression coincided with the expression pattern of ABI3. In plants ectopically expressing ABI3, AtPER1::GUS expression was found in true leaves, and AtPER1 could be induced by exogenous ABA and oxidative stress (H2O2 and hydroquinone). ABI3-mediated oxidative stress induction was dependent on the presence of an intact ARE element.

Cloning and computer analysis of the promoter region of the legumin-like storage protein gene from buckwheat, Fagopyrum esculentum Moench

Using the modified 5?-RACE approach, a fragment containing the 955 bp long 5?- regulatory region of the buckwheat storage globulin gene (FeLEG1) has been amplified from the genomic DNA of buckwheat. The entire fragment was sequenced and the sequence analyzed by computer prediction of cis-regulatory elements possibly involved in tissue specific and developmentally controlled seed storage protein gene expression. The promoter obtained might be interesting not only for fundamental research, but also as a useful tool for biotechnological application.

Regulation of gene expression of a cysteine proteinase, EP-C1, by a VIVIPAROUS1-like factor from common bean

A VIVIPAROUS1-like transcription factor, PvALF, is known to activate storage protein genes through the RY element in their promoters in maturing common bean seeds. This element also exists in the promoter of the gene for a cysteine proteinase, EP-C1, which is expressed in a germination-specific manner. We show that the EP-C1 gene expression is suppressed through interaction of PvALF with the RY element in the EP-C1 promoter.

ABA action and interactions in seeds

The recent discovery of genes involved in abscisic acid (ABA) biosynthesis and responses heralds a new era for seed physiology. Our understanding of the regulation of ABA biosynthesis is moving from a linear metabolic pathway to a spatial and temporal network that governs ABA action in seeds. Transcription factors involved in ABA signaling have been identified, together with their target sequences. This allows further analysis of the specificity of ABA signaling in a complex system of interacting factors.

Expression pattern of diacylglycerol acyltransferase-1, an enzyme involved in triacylglycerol biosynthesis, in Arabidopsis thaliana

Triacylglycerol (TAG) is the major carbon storage reserve in oilseeds such as Arabidopsis. Acyl-CoA:diacylglycerol acyltransferase (DGAT) catalyses the final step of the TAG synthesis pathway. Although TAG is mainly accumulated during seed development, and DGAT has presumably the highest activity in developing seeds, we show here that TAG synthesis is also actively taking place during germination and seedling development in Arabidopsis. The expression pattern of the DGAT1 gene was studied in transgenic plants containing the reporter gene beta-glucuronidase (GUS) fused with DNA sequences flanking the DGAT1 coding region. GUS activity was not only detected in developing seeds and pollen, which normally accumulate storage TAG, but also in germinating seeds and seedlings. Western blots showed that DGAT1 protein is present in several tissues, though is most abundant in developing seeds. In seedlings, DGAT1 is expressed in shoot and root apical regions, correlating with rapid cell division and growth. The expression of GUS in seedlings was consistent with the results of RNA gel blot analyses, precursor feeding and DGAT assay. In addition, DGAT1 gene expression is up-regulated by glucose and associated with glucose-induced changes in seedling development.

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.