Rice MYB protein OSMYB5 specifically binds to the AACA motif conserved among promoters of genes for storage protein glutelin

Orchestrating seed storage protein and starch accumulation toward overcoming yield-quality trade-off in cereal crops

Achieving high yield and good quality in crops is essential for human food security and health. However, there is usually disharmony between yield and quality. Seed storage protein (SSP) and starch, the predominant components in cereal grains, determine yield and quality, and their coupled synthesis causes a yield-quality trade-off. Therefore, dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality. Here, we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops, including maize, rice and wheat. We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights. We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding. Finally, future perspectives on major challenges are proposed.

Wheat NAC-A18 regulates grain starch and storage proteins synthesis and affects grain weight

KEY MESSAGE

Wheat NAC-A18 regulates both starch and storage protein synthesis in the grain, and a haplotype with positive effects on grain weight showed increased frequency during wheat breeding in China. Starch and seed storage protein (SSP) directly affect the processing quality of wheat grain. The synthesis of starch and SSP are also regulated at the transcriptional level. However, only a few starch and SSP regulators have been identified in wheat. In this study, we discovered a NAC transcription factor, designated as NAC-A18, which acts as a regulator of both starch and SSP synthesis. NAC-A18, is predominately expressed in wheat developing grains, encodes a transcription factor localized in the nucleus, with both activation and repression domains. Ectopic expression of wheat NAC-A18 in rice significantly decreased starch accumulation and increased SSP accumulation and grain size and weight. Dual-luciferase reporter assays indicated that NAC-A18 could reduce the expression of TaGBSSI-A1 and TaGBSSI-A2, and enhance the expression of TaLMW-D6 and TaLMW-D1. A yeast one hybrid assay demonstrated that NAC-A18 bound directly to the cis-element "ACGCAA" in the promoters of TaLMW-D6 and TaLMW-D1. Further analysis indicated that two haplotypes were formed at NAC-A18, and that NAC-A18_h1 was a favorable haplotype correlated with higher thousand grain weight. Based on limited population data, NAC-A18_h1 underwent positive selection during Chinese wheat breeding. Our study demonstrates that wheat NAC-A18 regulates starch and SSP accumulation and grain size. A molecular marker was developed for the favorable allele for breeding applications.

Regulation of seed storage protein synthesis in monocot and dicot plants: A comparative review

Seeds are a major source of nutrients for humans and animal livestock worldwide. With improved living standards, high nutritional quality has become one of the main targets for breeding. Storage protein content in seeds, which is highly variable depending on plant species, serves as a pivotal criterion of seed nutritional quality. In the last few decades, our understanding of the molecular genetics and regulatory mechanisms of storage protein synthesis has greatly advanced. Here, we systematically and comprehensively summarize breakthroughs on the conservation and divergence of storage protein synthesis in dicot and monocot plants. With regard to storage protein accumulation, we discuss evolutionary origins, developmental processes, characteristics of main storage protein fractions, regulatory networks, and genetic modifications. In addition, we discuss potential breeding strategies to improve storage protein accumulation and provide perspectives on some key unanswered problems that need to be addressed.

A new demethylase gene, OsDML4, is involved in high temperature-increased grain chalkiness in rice

High temperature (HT) can affect the accumulation of seed storage materials and cause adverse effects on the yield and quality of rice. DNA methylation plays an important role in plant growth and development. Here, we identified a new demethylase gene OsDML4 and discovered its function in cytosine demethylation to affect endosperm formation. Loss of function of OsDML4 induced chalky endosperm only under HT and dramatically reduced the transcription and accumulation of glutelins and 16 kDa prolamin. The expression of two transcription factor genes RISBZ1 and RPBF was significantly decreased in the osdml4 mutants, which caused adverse effects on the formation of protein bodies (PBs) with greatly decreased PB-II number, and incomplete and abnormally shaped PB-IIs. Whole-genome bisulfite sequencing analysis of seeds at 15 d after pollination revealed much higher global methylation levels of CG, CHG, and CHH contexts in the osdml4 mutants compared with the wild type. Moreover, the RISBZ1 promoter was hypermethylated but the RPBF promoter was almost unchanged under HT. No significant difference was detected between the wild type and osdml4 mutants under normal temperature. Our study demonstrated a novel OsDML4-mediated DNA methylation involved in the formation of chalky endosperm only under HT and provided a new perspective in regulating endosperm development and the accumulation of seed storage proteins in rice.

MaMYB4 is a negative regulator and a substrate of RING-type E3 ligases MaBRG2/3 in controlling banana fruit ripening

Fruit ripening is a complex developmental process, which is modulated by both transcriptional and post-translational events. Control of fruit ripening is important in maintaining moderate quality traits and minimizing postharvest deterioration. In this study, we discovered that the transcription factor MaMYB4 acts as a negative regulator of fruit ripening in banana. The protein levels of MaMYB4 decreased gradually with banana fruit ripening, paralleling ethylene production, and decline in firmness. DNA affinity purification sequencing combined with RNA-sequencing analyses showed that MaMYB4 preferentially binds to the promoters of various ripening-associated genes including ethylene biosynthetic and cell wall modifying genes. Furthermore, ectopic expression of MaMYB4 in tomato delayed tomato fruit ripening, which was accompanied by downregulation of ethylene biosynthetic and cell wall modifying genes. Importantly, two RING finger E3 ligases MaBRG2/3, whose protein accumulation increased progressively with fruit ripening, were found to interact with and ubiquitinate MaMYB4, contributing to decreased accumulation of MaMYB4 during fruit ripening. Transient overexpression of MaMYB4 and MaBRG2/3 in banana fruit ripening delayed or promoted fruit ripening by inhibiting or stimulating ethylene biosynthesis, respectively. Taken together, we demonstrate that MaMYB4 negatively modulates banana fruit ripening, and that MaMYB4 abundance could be regulated by protein ubiquitination, thus providing insights into the role of MaMYB4 in controlling fruit ripening at both transcriptional and post-translational levels.

Cereal Endosperms: Development and Storage Product Accumulation

The persistent triploid endosperms of cereal crops are the most important source of human food and animal feed. The development of cereal endosperms progresses through coenocytic nuclear division, cellularization, aleurone and starchy endosperm differentiation, and storage product accumulation. In the past few decades, the cell biological processes involved in endosperm formation in most cereals have been described. Molecular genetic studies performed in recent years led to the identification of the genes underlying endosperm differentiation, regulatory network governing storage product accumulation, and epigenetic mechanism underlying imprinted gene expression. In this article, we outline recent progress in this area and propose hypothetical models to illustrate machineries that control aleurone and starchy endosperm differentiation, sugar loading, and storage product accumulations. A future challenge in this area is to decipher the molecular mechanisms underlying coenocytic nuclear division, endosperm cellularization, and programmed cell death.

Comparison of the Agronomic, Cytological, Grain Protein Characteristics, as Well as Transcriptomic Profile of Two Wheat Lines Derived From Wild Emmer

Two advanced wheat lines BAd7-209 and BAd23-1 without the functional gene GPC-B1 were obtained from a cross between common wheat cultivar Chuannong 16 (CN16) and wild emmer wheat accession D97 (D97). BAd7-209 showed superior quality parameters than those of BAd23-1 and CN16. We found that the components of glutenins and gliadins in BAd7-209 and BAd23-1 were similar, whereas BAd7-209 had higher amount of glutenins and gliadins than those of BAd23-1. RNA sequencing analysis on developing grains of BAd7-209 and BAd23-1 as well as their parents revealed 382 differentially expressed genes (DEGs) between the high–grain protein content (GPC) (D97 + BAd7-209) and the low-GPC (CN16 + BAd23-1) groups. DEGs were mainly associated with transcriptional regulation of the storage protein genes, protein processing in endoplasmic reticulum, and protein export pathways. The upregulated gluten genes and transcription factors (e.g., NAC, MYB, and bZIP) may contribute to the high GPC in BAd7-209. Our results provide insights into the potential regulation pathways underlying wheat grain protein accumulation and contribute to make use of wild emmer for wheat quality improvement.

Rice seed storage proteins: Biosynthetic pathways and the effects of environmental factors

Rice (Oryza sativa L.) is the most important food crop for at least half of the world's population. Due to improved living standards, the cultivation of high-quality rice for different purposes and markets has become a major goal. Rice quality is determined by the presence of many nutritional components, including seed storage proteins (SSPs), which are the second most abundant nutrient components of rice grains after starch. Rice SSP biosynthesis requires the participation of multiple organelles and is influenced by the external environment, making it challenging to understand the molecular details of SSP biosynthesis and improve rice protein quality. In this review, we highlight the current knowledge of rice SSP biosynthesis, including a detailed description of the key molecules involved in rice SSP biosynthetic processes and the major environmental factors affecting SSP biosynthesis. The effects of these factors on SSP accumulation and their contribution to rice quality are also discussed based on recent findings. This recent knowledge suggests not only new research directions for exploring rice SSP biosynthesis but also innovative strategies for breeding high-quality rice varieties.

The MYB family transcription factor TuODORANT1 from Triticum urartu and the homolog TaODORANT1 from Triticum aestivum inhibit seed storage protein synthesis in wheat

Seed storage proteins (SSPs) are determinants of wheat end-product quality. SSP synthesis is mainly regulated at the transcriptional level. Few transcriptional regulators of SSP synthesis have been identified in wheat and this study aims to identify novel SSP gene regulators. Here, the R2R3 MYB transcription factor TuODORANT1 from Triticum urartu was found to be preferentially expressed in the developing endosperm during grain filling. In common wheat (Triticum aestivum) overexpressing TuODORANT1, the transcription levels of all the SSP genes tested by RNA-Seq analysis were reduced by 49.71% throughout grain filling, which contributed to 13.38%-35.60% declines in the total SSP levels of mature grains. In in vitro assays, TuODORANT1 inhibited both the promoter activities and the transcription of SSP genes by 1- to 13-fold. The electrophoretic mobility shift assay (EMSA) and ChIP-qPCR analysis demonstrated that TuODORANT1 bound to the cis-elements 5'-T/CAACCA-3' and 5'-T/CAACT/AG-3' in SSP gene promoters both in vitro and in vivo. Similarly, the homolog TaODORANT1 in common wheat hindered both the promoter activities and the transcription of SSP genes by 1- to 112-fold in vitro. Knockdown of TaODORANT1 in common wheat led to 14.73%-232.78% increases in the transcription of the tested SSP genes, which contributed to 11.43%-19.35% elevation in the total SSP levels. Our data show that both TuODORANT1 and TaODORANT1 are repressors of SSP synthesis.

A novel NAC family transcription factor SPR suppresses seed storage protein synthesis in wheat

The synthesis of seed storage protein (SSP) is mainly regulated at the transcriptional level. However, few transcriptional regulators of SSP synthesis have been characterized in common wheat (Triticum aestivum) owing to the complex genome. As the A genome donor of common wheat, Triticum urartu could be an elite model in wheat research considering its simple genome. Here, a novel NAC family transcription factor TuSPR from T. urartu was found preferentially expressed in developing endosperm during grain-filling stages. In common wheat transgenically overexpressing TuSPR, the content of total SSPs was reduced by c. 15.97% attributed to the transcription declines of SSP genes. Both in vitro and in vivo assays showed that TuSPR bound to the cis-element 5'-CANNTG-3' distributed in SSP gene promoters and suppressed the transcription. The homolog in common wheat TaSPR shared a conserved function with TuSPR on SSP synthesis suppression. The knock-down of TaSPR in common wheat resulted in 7.07%-20.34% increases in the total SSPs. Both TuSPR and TaSPR could be superior targets in genetic engineering to manipulate SSP content in wheat, and this work undoubtedly expands our knowledge of SSP gene regulation.

Multi-Locus GWAS of Quality Traits in Bread Wheat: Mining More Candidate Genes and Possible Regulatory Network

In wheat breeding, improved quality traits, including grain quality and dough rheological properties, have long been a critical goal. To understand the genetic basis of key quality traits of wheat, two single-locus and five multi-locus GWAS models were performed for six grain quality traits and three dough rheological properties based on 19, 254 SNPs in 267 bread wheat accessions. As a result, 299 quantitative trait nucleotides (QTNs) within 105 regions were identified to be associated with these quality traits in four environments. Of which, 40 core QTN regions were stably detected in at least three environments, 19 of which were novel. Compared with the previous studies, these novel QTN regions explained smaller phenotypic variation, which verified the advantages of the multi-locus GWAS models in detecting important small effect QTNs associated with complex traits. After characterization of the function and expression in-depth, 67 core candidate genes involved in protein/sugar synthesis, histone modification and the regulation of transcription factor were observed to be associated with the formation of grain quality, which showed that multi-level regulations influenced wheat grain quality. Finally, a preliminary network of gene regulation that may affect wheat quality formation was inferred. This study verified the power and reliability of multi-locus GWAS methods in wheat quality trait research, and increased the understanding of wheat quality formation mechanisms. The detected QTN regions and candidate genes in this study could be further used for gene cloning and marker-assisted selection in high-quality breeding of bread wheat.

ZmPBF and ZmGAMYB transcription factors independently transactivate the promoter of the maize (Zea mays) β-carotene hydroxylase 2 gene

The maize (Zea mays) enzyme β-carotene hydroxylase 2 (ZmBCH2) controls key steps in the conversion of β-carotene to zeaxanthin in the endosperm. The ZmBCH2 gene has an endosperm-preferred and developmentally regulated expression profile, but the detailed regulatory mechanism is unknown. To gain insight into the regulation of ZmBCH2, we isolated 2036 bp of the 5'-flanking region containing the 263 bp 5'-untranslated region (5'-UTR) including the first intron. We linked this to the β-glucuronidase reporter gene gusA. We found that high-level expression of gusA in rice seeds requires the 5'-UTR for enhanced activation. Truncated variants of the ZmBCH2 promoter retained their seed-preferred expression profile as long as a prolamin box and AACA motif were present. We identified candidate genes encoding the corresponding transcription factors (ZmPBF and ZmGAMYB) and confirmed that their spatiotemporal expression profiles are similar to ZmBCH2. Both ZmPBF and ZmGAMYB can transactivate ZmBCH2 expression in maize endosperm. To eliminate potential confounding effects in maize, we characterized the regulation of the minimal promoter region of ZmBCH2 in transgenic rice. This revealed that ZmPBF and ZmGAMYB independently transactivate the ZmBCH2 promoter. The mechanism that underpins our data provides an exciting new strategy for the control of target gene expression in engineered plants.

Nitrogen Supply Drives Senescence-Related Seed Storage Protein Expression in Rapeseed Leaves

In general, yield and fruit quality strongly rely on efficient nutrient remobilization during plant development and senescence. Transcriptome changes associated with senescence in spring oilseed rape grown under optimal nitrogen supply or mild nitrogen deficiency revealed differences in senescence and nutrient mobilization in old lower canopy leaves and younger higher canopy leaves [1]. Having a closer look at this transcriptome analyses, we identified the major classes of seed storage proteins (SSP) to be expressed in vegetative tissue, namely leaf and stem tissue. Expression of SSPs was not only dependent on the nitrogen supply but transcripts appeared to correlate with intracellular H₂O₂ contents, which functions as well-known signaling molecule in developmental senescence. The abundance of SSPs in leaf material transiently progressed from the oldest leaves to the youngest. Moreover, stems also exhibited short-term production of SSPs, which hints at an interim storage function. In order to decipher whether hydrogen peroxide also functions as a signaling molecule in nitrogen deficiency-induced senescence, we analyzed hydrogen peroxide contents after complete nitrogen depletion in oilseed rape and Arabidopsis plants. In both cases, hydrogen peroxide contents were lower in nitrogen deficient plants, indicating that at least parts of the developmental senescence program appear to be suppressed under nitrogen deficiency.

The wheat transcription factor TaGAMyb recruits histone acetyltransferase and activates the expression of a high-molecular-weight glutenin subunit gene

Glutenin proteins in wheat (Triticum aestivum L.) flour confer unique viscoelastic properties to dough products and, therefore, the concentration and composition of the glutenin proteins determine its end-use value. However, the mechanisms governing the glutenin gene expression remain elusive. In this study, we report that wheat TaGAMyb activates the high-molecular-weight glutenin subunit genes (TaGLU) through recruiting the histone acetyltransferase GCN5. By sequencing the promoters of TaGLU-1 genes from 40 modern wheat cultivars, we identified eight types of TaGAMyb binding motifs and verified these by electrophoretic mobility shift assays. The number of TaGAMyb binding motifs in TaGLU-1 genes is correlated with the abundance of glutenin in different cultivars. Chromatin immunoprecipitation plus polymerase chain reaction (ChIP-PCR) analysis reveals that TaGCN5 directly targets the promoters of TaGLU-1 genes in wheat endosperm. We find that TaGAMyb physically interacts with the wheat histone acetyltransferase TaGCN5 and also interacts with Arabidopsis thaliana AtGCN5. TaGAMyb ectopically expressed in Arabidopsis binds to the TaGLU-1Dy promoter on a TaGLU-1Dy transgene and activates its expression. AtGCN5 also targets the TaGLU-1Dy transgene and is involved in the establishment of acetylation at H3K9 and H3K14. These results demonstrate that TaGAMyb plays a dual role in activating expression of glutenin gene by directly binding to the TaGLU promoter and by recruiting GCN5 to modulate histone acetylation during wheat endosperm development.

Cloning and characterization of a multifunctional promoter from maize (Zea mays L.)

The use of tissue-specific promoters to drive the expression of target genes during certain developmental stages or in specific organs can prevent unnecessary gene expression caused by constitutive promoters. Utilizing heterologous promoters to regulate the expression of genes in transgenic receptors can help prevent gene silencing. Here, we engineered heterologous maize promoters that regulate gene-specific expression in rice plant receptors. We performed a histochemical and quantitative β-glucuronidase (GUS) analysis of the Zea mays legumin1 (ZM-LEGF) gene promoter and detailed detection of stably transformed rice expressing the GUS gene under the control of the promoter of ZM-LEGF (pZM-LEGF) and its truncated promoters throughout development. When the promoter sequence was truncated, the location and intensity of GUS expression changed. The results suggest that the sequence from -140 to +41 is a critical region that confers the expression of the entire promoter. Truncation of pZM-LEG (3'-deleted region of pZM-LEGF) markedly increased the GUS activity, with the core cis-elements located in the -273 to -140 regions, namely pZM-LEG6. Detailed analysis of pZM-LEG6::GUS T2 transformant rice seeds and plant tissues at different developmental stages indicated that this promoter is an ideal vegetative tissue-specific promoter that can serve as a valuable tool for transgenic rice breeding and genetic engineering studies.

Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits

The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.

A promoter analysis of MOTHER OF FT AND TFL1 1 (JcMFT1), a seed-preferential gene from the biofuel plant Jatropha curcas

MOTHER OF FT AND TFL1 (MFT)-like genes belong to the phosphatidylethanoamine-binding protein (PEBP) gene family in plants. In contrast to their homologs FLOWERING LOCUS T (FT)-like and TERMINAL FLOWER 1 (TFL1)-like genes, which are involved in the regulation of the flowering time pathway, MFT-like genes function mainly during seed development and germination. In this study, a full-length cDNA of the MFT-like gene JcMFT1 from the biodiesel plant Jatropha curcas (L.) was isolated and found to be highly expressed in seeds. The promoter of JcMFT1 was cloned and characterized in transgenic Arabidopsis. A histochemical β-glucuronidase (GUS) assay indicated that the JcMFT1 promoter was predominantly expressed in both embryos and endosperms of transgenic Arabidopsis seeds. Fluorometric GUS analysis revealed that the JcMFT1 promoter was highly active at the mid to late stages of seed development. After seed germination, the JcMFT1 promoter activity decreased gradually. In addition, both the JcMFT1 expression in germinating Jatropha embryos and its promoter activity in germinating Arabidopsis embryos were induced by abscisic acid (ABA), possibly due to two ABA-responsive elements, a G-box and an RY repeat, in the JcMFT1 promoter region. These results show that the JcMFT1 promoter is seed-preferential and can be used to control transgene expression in the seeds of Jatropha and other transgenic plants.

Functions of the CCCH type zinc finger protein OsGZF1 in regulation of the seed storage protein GluB-1 from rice

Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we describe a zinc finger gene of the Cys3His1 (CCCH or C3H) class, named OsGZF1, which was identified in a yeast one-hybrid screening using the core promoter region of GluB-1 as bait and cDNA expression libraries prepared from developing rice panicles and grains as prey. The OsGZF1 protein binds specifically to the bait sequence in yeast and this interaction was confirmed in vitro. OsGZF1 is predominantly expressed in a confined domain surrounding the scutellum of the developing embryo and is localised in the nucleus. Transient expression experiments demonstrated that OsGZF1 can down-regulate a GluB-1-GUS (β-glucuronidase) reporter and OsGZF1 was also able to significantly reduce activation conferred by RISBZ1 which is a known strong GluB-1 activator. Furthermore, down-regulation of OsGZF1 by an RNAi approach increased grain nitrogen concentration. We propose that OsGZF1 has a function in regulating the GluB-1 promoter and controls accumulation of glutelins during grain development.

A valid strategy for precise identifications of transcription factor binding sites in combinatorial regulation using bioinformatic and experimental approaches

BACKGROUND

Transcription factor (TF) binding sites (cis element) play a central role in gene regulation, and eukaryotic organisms frequently adapt a combinatorial regulation to render sophisticated local gene expression patterns. Knowing the precise cis element on a distal promoter is a prerequisite for studying a typical transcription process; however, identifications of cis elements have lagged behind those of their associated trans acting TFs due to technical difficulties. Consequently, gene regulations via combinatorial TFs, as widely observed across biological processes, have remained vague in many cases.

RESULTS

We present here a valid strategy for identifying cis elements in combinatorial TF regulations. It consists of bioinformatic searches of available databases to generate candidate cis elements and tests of the candidates using improved experimental assays. Taking the MYB and the bHLH that collaboratively regulate the anthocyanin pathway genes as examples, we demonstrate how candidate cis motifs for the TFs are found on multi-specific promoters of chalcone synthase (CHS) genes, and how to experimentally test the candidate sites by designing DNA fragments hosting the candidate motifs based on a known promoter (us1 allele of Ipomoea purpurea CHS-D in our case) and applying site-mutagenesis at the motifs. It was shown that TF-DNA interactions could be unambiguously analyzed by assays of electrophoretic mobility shift (EMSA) and dual-luciferase transient expressions, and the resulting evidence precisely delineated a cis element. The cis element for R2R3 MYBs including Ipomoea MYB1 and Magnolia MYB1, for instance, was found to be ANCNACC, and that for bHLHs (exemplified by Ipomoea bHLH2 and petunia AN1) was CACNNG. A re-analysis was conducted on previously reported promoter segments recognized by maize C1 and apple MYB10, which indicated that cis elements similar to ANCNACC were indeed present on these segments, and tested positive for their bindings to Ipomoea MYB1.

CONCLUSION

Identification of cis elements in combinatorial regulation is now feasible with the strategy outlined. The working pipeline integrates the existing databases with experimental techniques, providing an open framework for precisely identifying cis elements. This strategy is widely applicable to various biological systems, and may enhance future analyses on gene regulation.

Role of conserved non-coding regulatory elements in LMW glutenin gene expression

Transcriptional regulation of LMW glutenin genes were investigated in-silico, using publicly available gene sequences and expression data. Genes were grouped into different LMW glutenin types and their promoter profiles were determined using cis-acting regulatory elements databases and published results. The various cis-acting elements belong to some conserved non-coding regulatory regions (CREs) and might act in two different ways. There are elements, such as GCN4 motifs found in the long endosperm box that could serve as key factors in tissue-specific expression. Some other elements, such as the AACA/TA motifs or the individual prolamin box variants, might modulate the level of expression. Based on the promoter sequences and expression characteristic LMW glutenin genes might be transcribed following two different mechanisms. Most of the s- and i-type genes show a continuously increasing expression pattern. The m-type genes, however, demonstrate normal distribution in their expression profiles. Differences observed in their expression could be related to the differences found in their promoter sequences. Polymorphisms in the number and combination of cis-acting elements in their promoter regions can be of crucial importance in the diverse levels of production of single LMW glutenin gene types.

The vacuolar processing enzyme OsVPE1 is required for efficient glutelin processing in rice

Rice (Oryza sativa L.) accumulates prolamines and glutelins as its major storage proteins. Glutelins are synthesized on rough endoplasmic reticulum as 57-kDa precursors; they are then sorted into protein storage vacuoles where they are processed into acidic and basic subunits. We report a novel rice glutelin mutant, W379, which accumulates higher levels of the 57-kDa glutelin precursor. Genetic analysis revealed that the W379 phenotype is controlled by a single recessive nuclear gene. Using a map-based cloning strategy, we identified this gene, OsVPE1, which is a homolog of the Arabidopsis betaVPE gene. OsVPE1 encodes a 497-amino-acid polypeptide. Nucleotide sequence analysis revealed a missense mutation in W379 that changes Cys269 to Gly. Like the wild-type protein, the mutant protein is sorted into vacuoles; however, the enzymatic activity of the mutant OsVPE1 is almost completely eliminated. Further, we show that OsVPE1 is incorrectly cleaved, resulting in a mature protein that is smaller than the wild-type mature protein. Taken together, these results demonstrate that OsVPE1 is a cysteine protease that plays a crucial role in the maturation of rice glutelins. Further, OsVPE1 Cys269 is a key residue for maintaining the Asn-specific cleavage activity of OsVPE1.

Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling

Legume seeds represent a major source of proteins for human and livestock diets. The model legume Medicago truncatula is characterized by a process of seed development very similar to that of other legumes, involving the interplay of sets of transcription factors (TFs). Here, we report the first expression profiling of over 700 M. truncatula genes encoding putative TFs throughout seven stages of seed development, obtained using real-time quantitative RT-PCR. A total of 169 TFs were selected which were expressed at late embryogenesis, seed filling or desiccation. The site of expression within the seed was examined for 41 highly expressed transcription factors out of the 169. To identify possible target genes for these TFs, the data were combined with a microarray-derived transcriptome dataset. This study identified 17 TFs preferentially expressed in individual seed tissues and 135 corresponding co-expressed genes, including possible targets. Certain of the TFs co-expressed with storage protein mRNAs correspond to those already known to regulate seed storage protein synthesis in Arabidopsis, whereas the timing of expression of others may be more specifically related to the delayed expression of the legumin-class storage proteins observed in legumes.

Spatial and temporal expression of endosperm transfer cell-specific promoters in transgenic rice and barley

Two putative endosperm-specific rice genes, OsPR602 and OsPR9a, were identified from database searches. The promoter regions of these genes were isolated, and transcriptional promoter:beta-glucuronidase (GUS) fusion constructs were stably transformed into rice and barley. The GUS expression patterns revealed that these promoters were active in early grain development in both rice and barley, and showed strongest expression in endosperm transfer cells during the early stages of grain filling. The GUS expression was similar in both rice and barley, but, in barley, expression was exclusively in the endosperm transfer cells and differed in timing of activation relative to rice. In rice, both promoters showed activity not only in the endosperm transfer cells, but also in the transfer cells of maternal tissue and in several floral tissues shortly before pollination. The expression patterns of OsPR602 and OsPR9a in flowers differed. The similarity of expression in both rice and barley suggests that these promoters may be useful to control transgene expression in the transfer cells of cereal grains with the aim of altering nutrient uptake or enhancing the barrier against pathogens at the boundary between maternal tissue and the developing endosperm. However, the expression during floral development should be considered if the promoters are used in rice.

Wheat Dof transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development

Wheat prolamin-box binding factor (WPBF), a DOF transcription factor previously was isolated from wheat endosperm and suggested to function as an activator of prolamin gene expression during seed development. In this study, we showed that WPBF is expressed in all wheat tissues analyzed, and a protein, TaQM, was identified from a wheat root cDNA library, to interact with the Dof domain of WPBF. The specific interaction between WPBF and TaQM was confirmed by pull-down assay and bimolecular fluorescence complementation (BiFC) experiment. The expression patterns of TaQM gene are similar with that of WPBF. The GST-WPBF expressed in bacteria binds the Prolamin box (PB) 5'-TGTAAAG-3', derived from the promoter region of a native alpha-gliadin gene encoding a storage protein. Transient expression experiments in co-transfected BY-2 protoplast cells demonstrated that WPBF trans-activated transcription from native alpha-gliadin promoter through binding to the intact PB. When WPBF and TaQM are co-transfected together the transcription activity of alpha-gliadin gene was six-fold higher than when WPBF was transfected alone. Furthermore, the promoter activities of WPBF gene were observed in the seeds and the vascular system of transgenic Arabidopsis, which was identical to the expression profiles of WPBF in wheat. Hence, we proposed that WPBF functions not only during wheat seed development but also during other growth and development processes.

Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes

The Dof (DNA binding with one finger) transcriptional activator rice (Oryza sativa) prolamin box binding factor (RPBF), which is involved in gene regulation of rice seed storage proteins, has been isolated from rice cDNA expressed sequence tag clones containing the conserved Dof. RPBF is found as a single gene per haploid genome. Comparison of RPBF genomic and cDNA sequences revealed that the genomic copy is interrupted by one long intron of 1,892 bp in the 5' noncoding region. We demonstrated by transient expression in rice callus protoplasts that the isolated RPBF trans-activated several storage protein genes via an AAAG target sequence located within their promoters, and with methylation interference experiments the additional AAAG-like sequences in promoters of genes expressed in maturing seeds were recognized by the RPBF protein. Binding was sequence specific, since mutation of the AAAG motif or its derivatives decreased both binding and trans-activation by RPBF. Synergism between RPBF and RISBZ1 recognizing the GCN4 motif [TGA(G/C)TCA] was observed in the expression of many storage protein genes. Overexpression of both transcription factors gave rise to much higher levels of expression than the sum of individual activities elicited by either RPBF or RISBZ1 alone. Furthermore, mutation of recognition sites suppressed reciprocal trans-activation ability, indicating that there are mutual interactions between RISBZ1 and RPBF. The RPBF gene is predominantly expressed in maturing endosperm and coordinately expressed with seed storage protein genes, and is involved in the quantitative regulation of genes expressed in the endosperm in cooperation with RISBZ1.

Ternary complex formation between HvMYBS3 and other factors involved in transcriptional control in barley seeds

The SHAQKYF R1MYB transcription factor (TF) HvMYBS3 from barley is an activator of gene expression both during endosperm development and in aleurone cells upon seed germination. Its mRNA was detected as early as 10 days after flowering in developing barley endosperm, with a peak at 18 days, and in aleurone cells at 8 h after water imbibition, as shown by Northern blot and in situ hybridization analyses. The HvMYBS3 protein expressed in bacteria binds to oligonucleotides containing a GATA core derived from the promoters of: (i) the developing endosperm gene Itr1 (5'-GATAAGATA-3') encoding trypsin inhibitor BTI-CMe, and (ii) the post-germinating aleurone gene Amy6.4 (5'-TATCCAC-3'/5'-GTGGATA-3') encoding a high-pI alpha-amylase. Transient expression experiments in co-bombarded developing endosperms and in barley aleurone layers demonstrated that HvMYBS3 trans-activated transcription both from Itr1 and Amy6.4 promoters, in contrast with a previously reported seed-expressed R1MYB, HvMCB1, which was an activator of Itr1 and a transcriptional repressor of the Amy6.4 gene. In the yeast three-hybrid system, the HvMYBS3 protein formed a ternary complex with BPBF and BLZ2, two important seed TFs. However, no binary interactions could be detected between HvMYBS3 and BLZ2 or between HvMYBS3 and BPBF.

Single nucleotide polymorphism, genetic mapping, and expression of genes coding for the DOF wheat prolamin-box binding factor

Wheat prolamin-box binding factor (WPBF) was shown to be an activator of Triticum aestivum L. storage protein genes. Three homoeologous genes encoding this transcription factor were isolated from a bacterial artificial chromosome genomic library and sequenced. The genes all have two exons separated by an intron of approximately 1,000 bp where the second exon contains the entire coding sequence. Many differences were found between homoeologous sequences, but none of them is predicted to significantly alter the sequence of the putative encoded protein. The three homoeologous genes are specifically expressed in grain from 3 to 39 days after anthesis. The allelic variation of a genetically diverse collection of 27 bread wheat lines was assessed. One, five, and one single-nucleotide polymorphisms (SNPs) were detected in the wPbf genes for the A, B, and D genomes, respectively. Physical and genetic mapping utilizing some of the SNPs identified confirmed that wPbf genes are located close to the centromeres on the homoeologous group 5 chromosomes. The low level of allelic diversity found in wPbf genes may suggest that these genes play a key role and are thus constrained by selection.

HvMCB1, a R1MYB transcription factor from barley with antagonistic regulatory functions during seed development and germination

The functional analysis of hydrolase gene promoters induced by gibberellin (GA) in barley aleurone cells upon germination has identified a tripartite GA-response complex (GARC) containing a 5'-TATCCAC-3' box as well as the GA-responsive element (GARE) recognized by GAMYB and the pyrimidine box interacting with the DOF transcription factors BPBF and SAD. We show here that the MCB1 gene encoding a R1MYB protein binds to the 5'-TATCCAC-3' (GATA core) box in vitro and is a transcriptional repressor of a GA-induced amylase (Amy6.4) promoter in bombarded aleurone layers. Northern blot and mRNA in situ hybridization analyses showed that the MCB1 transcripts accumulate in the aleurone cells upon germination, as well as in endosperm tissues during seed development. The HvMCB1 protein expressed in bacteria binds in a specific manner to a 27-mer oligonucleotide containing the 5'-TATCCAC-3' sequence, derived from the promoter region of the Amy6.4 gene. Accumulation of the MCB1 transcript diminished in response to external GA incubation in aleurone cells, and in transient expression experiments HvMCB1 repressed transcription of the Amy6.4 promoter in GA-treated aleurone layers and reversed the GAMYB-mediated activation of this amylase promoter. In contrast, during endosperm maturation HvMCB1 acted as a transcription activator of the seed-specific Itr1 gene promoter through binding to a 5'-GATAAGATA-3' box.

Genomic structures and characterization of the 5'-flanking regions of acyl carrier protein and Delta4-palmitoyl-ACP desaturase genes from Coriandrum sativum

The seed-specific or seed-predominant promoters of acyl carrier protein (Cs-ACP1) and Delta4-palmitoyl-acyl carrier protein desaturase (Cs-4PAD) genes, which are involved in the biosynthesis of petroselinic acid, were isolated from coriander (Coriandrum sativum) and analyzed in coriander endosperms and transgenic Arabidopsis. The expression of Cs-ACP1 and Cs-4PAD genes was coordinately regulated during seed development.

The DOF protein, SAD, interacts with GAMYB in plant nuclei and activates transcription of endosperm-specific genes during barley seed development

The DOF protein, SAD, previously shown to be a transcriptional activator in barley aleurone cells upon seed germination, also has an important role in gene regulation during endosperm development. mRNA was detected in early (10 days after flowering) developing barley seeds where it accumulated in the starchy endosperm, aleurone cells, nucellar projection, vascular tissues and the immature embryo, as shown by RT-PCR and in situ hybridization analyses. The SAD protein, expressed in bacteria, binds to oligonucleotides containing the prolamine box, 5'-A/TAAAG-3'sequence, derived from the promoter regions of the endosperm-specific genes Hor2 and Itr1, encoding a B-hordein and trypsin-inhibitor BTI-CMe, respectively. SAD competed for the same binding sites with another endosperm-expressed DOF protein, BPBF. Transient expression experiments in co-bombarded developing endosperms demonstrated that SAD trans-activated transcription from Hor2 and Itr1 promoters through binding to the intact DOF motifs. When the two DOF factors are co-bombarded together an additive effect was observed upon the expression of the Itr1 gene. In-frame fusion of the Sad ORF to the reporter green fluorescent protein gene directs the fluorescence expression to the nucleus in transiently transformed onion epidermal layers. The visualization of fluorescence in the nucleus of onion cells, using the bimolecular fluorescent complex (BiFC) approach, has shown the in vivo interaction between SAD and the R2R3MYB protein GAMYB. The interaction in plant cells has also been documented for the DOF protein BPBF and GAMYB, but nuclear interaction could not be detected between BPBF and SAD by this procedure.

Different mechanisms participate in the R-dependent activity of the R2R3 MYB transcription factor C1

The R2R3 MYB transcription factor C1 requires the basic helix-loop-helix factor R as an essential co-activator for the transcription of maize anthocyanin genes. In contrast, the R2R3 MYB protein P1 activates a subset of the C1-regulated genes independently of R. Substitution of six amino acids in P1 with the C1 amino acids results in P1(*), whose activity on C1-regulated and P1-regulated genes is R-dependent or R-enhanced, respectively. We have used P1(*) in combination with various promoters to uncover two mechanisms for R function. On synthetic promoters that contain only C1/P1 binding sites, R is an essential co-activator of C1. This function of R is unlikely to simply be the result of an increase in the C1 DNA-binding affinity, since transcriptional activity of a C1 mutant that binds DNA at a higher affinity, comparable with P1, remains R-dependent. The differential transcriptional activity of C1 fusions with the yeast Gal4 DNA-binding domain in yeast and maize cells suggests that part of the function of R is to relieve C1 from a plant-specific inhibitor. A second function of R requires cis-regulatory elements in addition to the C1/P1 DNA-binding sites for R-enhanced transcription of a1. We hypothesize that R functions in this mode by binding or recruiting additional factors to the anthocyanin regulatory element conserved in the promoters of several anthocyanin genes. Together, these findings suggest a model in which combinatorial interactions with co-activators enable R2R3 MYB factors with very similar DNA binding preferences to discriminate between target genes in vivo.

Synergistic activation of seed storage protein gene expression in Arabidopsis by ABI3 and two bZIPs related to OPAQUE2

The expression of many seed storage protein genes in cereals relies on transcription factors of the bZIP class, belonging to the maize OPAQUE2 family. Here, we describe a survey of such factors in the genome of Arabidopsis thaliana, and the characterization of two of them, AtbZIP10 and AtbZIP25. Expression analysis by in situ hybridization shows that the occurrence of their mRNAs in the seed starts from early stages of development, peaks at maturation, and declines later in seed development, matching temporally and spatially those of the seed storage protein genes encoding 2S albumins and cruciferins. Gel mobility shift assays showed that AtbZIP10 and AtbZIP25 bind the ACGT boxes present in At2S and CRU3 promoters. Moreover, using the yeast two-hybrid system we show that AtbZIP10 and AtbZIP25 can interact in vivo with ABI3, an important regulator of gene expression in the seed of Arabidopsis. Transient expression analyses of a reporter gene under the control of the At2S1 promoter in transgenic plants overexpressing ectopically AtbZIP10, AtbZIP25, and ABI3 reveal that none of these factors could activate significantly the reporter gene when expressed individually. However, co-expression of AtbZIP10/25 with ABI3 resulted in a remarkable increase in the activation capacity over the At2S1 promoter, suggesting that they are part of a regulatory complex involved in seed-specific expression. This study shows a common mechanism of ABI3 in regulating different seed-specific genes through combinatorial interactions with particular bZIP proteins and a conserved role of O2-like bZIPs in monocot and dicot species.

The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development

HvGAMYB, a MYB transcription factor previously shown to be expressed in barley aleurone cells in response to gibberellin during germination, also has an important role in gene regulation during endosperm development. The mRNA was detected early (10 DAF) in the seeds where it accumulates, not only in the aleurone layer, starchy endosperm, nucellar projection and vascular tissue, but also in the immature embryo as shown by in situ hybridization analysis. The HvGAMYB protein, expressed in bacteria, binds to oligonucleotides containing the 5'-TAACAAC-3' or 5'-CAACTAAC-3' sequences, derived from the promoter regions of the endosperm-specific genes Hor2 and Itr1, encoding a B-hordein and trypsin-inhibitor BTI-CMe, respectively. Binding is prevented when these motifs are mutated to 5'-TgACAAg-3' and 5'-CgACTgAC-3'. Transient expression experiments in co-bombarded developing endosperms demonstrate that HvGAMYB trans-activates transcription from native Hor2 and Itr1 promoters through binding to the intact motifs described above. Trans-activation of the Hor2 promoter also requires an intact prolamine box (PB). This suggests that HvGAMYB interacts in developing barley endosperms with the PB-binding factor BPBF, an endosperm-specific DOF transcriptional activator of the Hor2 gene. The in vivo interaction experiment between HvGAMYB and BPBF was done in the yeast two-hybrid system, where HvGAMYB potentiates the BPBF trans-activation capacity through interaction with its C-terminal domain.

A rice functional transcriptional activator, RISBZ1, responsible for endosperm-specific expression of storage protein genes through GCN4 motif

The GCN4 motif, a cis-element that is highly conserved in the promoters of cereal seed storage protein genes, plays a central role in controlling endosperm-specific expression. This motif is the recognition site for a basic leucine zipper transcriptional factor that belongs to the group of maize Opaque-2 (O2)-like proteins. Five different basic leucine zipper cDNA clones, designated RISBZ1-5, have been isolated from a rice seed cDNA library. The predicted gene products can be divided into two groups based on their amino acid sequences. Although all the RISBZ proteins are able to interact with the GCN4 motif, only RISBZ1 is capable of activating (more than 100-fold expression) the expression of a reporter gene under a minimal promoter fused to a pentamer of the GCN4 motif. Loss-of-function and gain-of-function experiments using the yeast GAL4 DNA binding domain revealed that the proline-rich N-terminal domain (27 amino acids in length) is responsible for transactivation. The RISBZ1 protein is capable of forming homodimers as well as heterodimers with other RISBZ subunit proteins. RISBZ1 gene expression is restricted to the seed, where it precedes the expression of storage protein genes. When the RISBZ1 promoter was transcriptionally fused to the beta-glucuronidase reporter gene and the chimeric gene was introduced into rice, the beta-glucuronidase gene is specifically expressed in aleurone and subaleurone layer of the developing endosperm. These findings suggest that the specific expression of transcriptional activator RISBZ1 gene may determine the endosperm specificity of the storage protein genes.

Human Cdc5, a regulator of mitotic entry, can act as a site-specific DNA binding protein

G(2)/M progression requires coordinated expression of many gene products, but little is known about the transcriptional regulators involved. We recently identified human Cdc5, a positive regulator of G(2)/M in mammalian cells. We also demonstrated the presence of a latent activation domain in its carboxyl terminus, suggesting that human Cdc5 regulates G(2)/M through transcriptional activation. Despite the presence of a DNA binding domain, studies by others have failed to identify a preferential binding site for Cdc5 family members. In addition, Cdc5 recently has been associated with the splicesome in several organisms, suggesting that it may not act through DNA binding. We now report the identification of a 12 bp sequence to which human Cdc5 binds specifically and with high affinity through its amino terminus. We show that this DNA-protein interaction is capable of activating transcription. We also used a selection system in yeast to identify human genomic fragments that interact with human Cdc5. Several of these contained sequences similar to the binding site. We demonstrate that these bind human Cdc5 with similar specificity and affinity. These experiments provide the first evidence that Cdc5 family members can act as site-specific DNA binding proteins, and that human Cdc5 may interact with specific, low abundance sequences in the human genome. This raises the possibility that Cdc5 proteins may participate in more than one process necessary for regulated cell division.

Quantitative nature of the Prolamin-box, ACGT and AACA motifs in a rice glutelin gene promoter: minimal cis-element requirements for endosperm-specific gene expression

The -197 bp promoter of the rice seed storage protein gene, GluB-1, is capable of conferring endosperm-specific gene expression. This proximal 5' flanking region contains four motifs, GCN4, AACA, ACGT and Prolamin-box, which are conserved in many seed storage protein genes. We previously showed that multiple copies of GCN4 conferred endosperm expression pattern when fused to the -46 core promoter of CaMV 35S. In this paper we demonstrate, using a similar approach, that tandem repeated copies of any of the other three motifs are unable to direct expression in seeds as well as other tissues of transgenic rice plants. Mutational analysis of individual motifs in the -197 bp promoter resulted in remarkable reductions in promoter activity. These results indicate that the GCN4 motif acts as an essential element determining endosperm-specific expression and that the AACA, ACGT and Prolamin-box are involved in quantitative regulation of the GluB-1 gene. A set of gain-of-function experiments using transgenic rice showed that either the Prolamin-box or AACA, although often coupled with GCN4 in many genes, is insufficient to form a functional promoter unit with GCN4, whereas a combination of GCN4, AACA and ACGT motifs was found sufficient to confer a detectable level of endosperm expression. Taken together, our results provide direct insight into the importance of combinatorial interplay between cis-elements in regulating the expression of seed storage protein genes.