Transcriptional and post-transcriptional regulation of soybean seed protein mRNA levels

Soybean genetic resources contributing to sustainable protein production

KEY MESSAGE

Genetic resources contributes to the sustainable protein production in soybean. Soybean is an important crop for food, oil, and forage and is the main source of edible vegetable oil and vegetable protein. It plays an important role in maintaining balanced dietary nutrients for human health. The soybean protein content is a quantitative trait mainly controlled by gene additive effects and is usually negatively correlated with agronomic traits such as the oil content and yield. The selection of soybean varieties with high protein content and high yield to secure sustainable protein production is one of the difficulties in soybean breeding. The abundant genetic variation of soybean germplasm resources is the basis for overcoming the obstacles in breeding for soybean varieties with high yield and high protein content. Soybean has been cultivated for more than 5000 years and has spread from China to other parts of the world. The rich genetic resources play an important role in promoting the sustainable production of soybean protein worldwide. In this paper, the origin and spread of soybean and the current status of soybean production are reviewed; the genetic characteristics of soybean protein and the distribution of resources are expounded based on phenotypes; the discovery of soybean seed protein-related genes as well as transcriptomic, metabolomic, and proteomic studies in soybean are elaborated; the creation and utilization of high-protein germplasm resources are introduced; and the prospect of high-protein soybean breeding is described.

Genomic regions associated with important seed quality traits in food-grade soybeans

BACKGROUND

The production of soy-based food products requires specific physical and chemical characteristics of the soybean seed. Identification of quantitative trait loci (QTL) associated with value-added traits, such as seed weight, seed protein and sucrose concentration, could accelerate the development of competitive high-protein soybean cultivars for the food-grade market through marker-assisted selection (MAS). The objectives of this study were to identify and validate QTL associated with these value-added traits in two high-protein recombinant inbred line (RIL) populations.

RESULTS

The RIL populations were derived from the high-protein cultivar 'AC X790P' (49% protein, dry weight basis), and two high-yielding commercial cultivars, 'S18-R6' (41% protein) and 'S23-T5' (42% protein). Fourteen large-effect QTL (R2 > 10%) were identified associated with seed protein concentration. Of these QTL, seven QTL were detected in both populations, and eight of them were co-localized with QTL associated with either seed sucrose concentration or seed weight. None of the protein-related QTL was found to be associated with seed yield in either population. Sixteen candidate genes with putative roles in protein metabolism were identified within seven of these protein-related regions: qPro_Gm02-3, qPro_Gm04-4, qPro_Gm06-1, qPro_Gm06-3, qPro_Gm06-6, qPro_Gm13-4 and qPro-Gm15-3.

CONCLUSION

The use of RIL populations derived from high-protein parents created an opportunity to identify four novel QTL that may have been masked by large-effect QTL segregating in populations developed from diverse parental cultivars. In total, we have identified nine protein QTL that were detected either in both populations in the current study or reported in other studies. These QTL may be useful in the curated selection of new soybean cultivars for optimized soy-based food products.

Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

BACKGROUND

Little is known about the molecular basis of seed size formation in endospermic seed of dicotyledons. The seed of castor bean (Ricinus communis L.) is considered as a model system in seed biology studies because of its persistent endosperms throughout seed development.

RESULTS

We compared the size of endosperm and endospermic cells between ZB107 and ZB306 and found that the larger seed size of ZB107 resulted from a higher cell count in the endosperm, which occupy a significant amount of the total seed volume. In addition, fresh weight, dry weight, and protein content of seeds were remarkably higher in ZB107 than in ZB306. Comparative proteomic and transcriptomic analyses were performed between large-seed ZB107 and small-seed ZB306, using isobaric tags for relative and absolute quantification (iTRAQ) and RNA-seq technologies, respectively. A total of 1416 protein species were identified, of which 173 were determined as differentially abundant protein species (DAPs). Additionally, there were 9545 differentially expressed genes (DEGs) between ZB306 and ZB107. Functional analyses revealed that these DAPs and DEGs were mainly involved in cell division and the metabolism of carbohydrates and proteins.

CONCLUSIONS

These findings suggest that both cell number and storage-component accumulation are critical for the formation of seed size, providing new insight into the potential mechanisms behind seed size formation in endospermic seeds.

Meta-analysis and transcriptome profiling reveal hub genes for soybean seed storage composition during seed development

Soybean is an important crop providing edible oil and protein source. Soybean oil and protein contents are quantitatively inherited and significantly affected by environmental factors. In this study, meta-analysis was conducted based on soybean physical maps to integrate quantitative trait loci (QTLs) from multiple experiments in different environments. Meta-QTLs for seed oil, fatty acid composition, and protein were identified. Of them, 11 meta-QTLs were located on hot regions for both seed oil and protein. Next, we selected 4 chromosome segment substitution lines with different seed oil and protein contents to characterize their 3 years of phenotype selection in the field. Using strand-specific RNA-sequencing analysis, we profile the time-course transcriptome patterns of soybean seeds at early maturity, middle maturity, and dry seed stages. Pairwise comparison and K-means clustering analysis revealed 7,482 differentially expressed genes and 45 expression patterns clusters. Weighted gene coexpression network analysis uncovered 46 modules of gene expression patterns. The 2 most significant coexpression networks were visualized, and 7 hub genes were identified that were involved in soybean oil and seed storage protein accumulation processes. Our results provided a transcriptome dataset for soybean seed development, and the candidate hub genes represent a foundation for further research.

Ribosome profiling reveals changes in translational status of soybean transcripts during immature cotyledon development

To understand translational capacity on a genome-wide scale across three developmental stages of immature soybean seed cotyledons, ribosome profiling was performed in combination with RNA sequencing and cluster analysis. Transcripts representing 216 unique genes demonstrated a higher level of translational activity in at least one stage by exhibiting higher translational efficiencies (TEs) in which there were relatively more ribosome footprint sequence reads mapping to the transcript than were present in the control total RNA sample. The majority of these transcripts were more translationally active at the early stage of seed development and included 12 unique serine or cysteine proteases and 16 2S albumin and low molecular weight cysteine-rich proteins that may serve as substrates for turnover and mobilization early in seed development. It would appear that the serine proteases and 2S albumins play a vital role in the early stages. In contrast, our investigation of profiles of 19 genes encoding high abundance seed storage proteins, such as glycinins, beta-conglycinins, lectin, and Kunitz trypsin inhibitors, showed that they all had similar patterns in which the TE values started at low levels and increased approximately 2 to 6-fold during development. The highest levels of these seed protein transcripts were found at the mid-developmental stage, whereas the highest ribosome footprint levels of only up to 1.6 TE were found at the late developmental stage. These experimental findings suggest that the major seed storage protein coding genes are primarily regulated at the transcriptional level during normal soybean cotyledon development. Finally, our analyses also identified a total of 370 unique gene models that showed very low TE values including over 48 genes encoding ribosomal family proteins and 95 gene models that are related to energy and photosynthetic functions, many of which have homology to the chloroplast genome. Additionally, we showed that genes of the chloroplast were relatively translationally inactive during seed development.

Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development

We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period. An Arabidopsis ddcc mutant lacking CHH and CHG methylation does not affect seed development, germination, or major patterns of gene expression, implying that CHH and CHG methylation does not play a significant role in seed development or in regulating seed gene activity. By contrast, over 100 TEs are transcriptionally de-repressed in ddcc seeds, suggesting that the increase in CHH-context methylation may be a failsafe mechanism to reinforce transposon silencing. Many genes encoding important classes of seed proteins, such as storage proteins, oil biosynthesis enzymes, and transcription factors, reside in genomic regions devoid of methylation at any stage of seed development. Many other genes in these classes have similar methylation patterns, whether the genes are active or repressed. Our results suggest that methylation does not play a significant role in regulating large numbers of genes important for programming seed development in both soybean and Arabidopsis. We conclude that understanding the mechanisms controlling seed development will require determining how cis-regulatory elements and their cognate transcription factors are organized in genetic regulatory networks.

PP2C-like Promoter and Its Deletion Variants Are Induced by ABA but Not by MeJA and SA in Arabidopsis thaliana

Gene expression is mediated through interaction between cis regulatory elements and its cognate transcription factors. Cis regulatory elements are defined as non-coding DNA sequences that provide the binding sites for transcription factors and are clustered in the upstream region of genes. ACGT cis regulatory element is one of the important cis regulatory elements found to be involved in diverse biological processes like auxin response, salicylic acid (SA) response, UV light response, ABA response and jasmonic acid (JA) response. We identified through in silico analysis that the upstream region of protein phosphatase 2C (PP2C) gene has a distinct genetic architecture of ACGT elements. In the present study, the activation of the full length promoter and its deletion constructs like 900 base pair, 500 base pair, 400 base pair and NRM (Nathji Rajesh Mehrotra) were examined by stable transformation in Arabidopsis thaliana using β-glucuronidase as the reporter gene. Evaluation of deletion constructs of PP2C-like promoter was carried out in the presence of phytohormones like abscisic acid (ABA), SA and JA. Our result indicated that the full length and 900 base pair promoter-reporter constructs of PP2C-like promoter was induced in response to ABA but not to methyl jasmonate and SA.

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.

Organ accumulation and subcellular location of Cicer arietinum ST1 protein

The ST (ShooT Specific) proteins are a new family of proteins characterized by a signal peptide, tandem repeats of 25/26 amino acids, and a domain of unknown function (DUF2775), whose presence is limited to a few families of dicotyledonous plants, mainly Fabaceae and Asteraceae. Their function remains unknown, although involvement in plant growth, fruit morphogenesis or in biotic and abiotic interactions have been suggested. This work is focused on ST1, a Cicer arietinum ST protein. We established the protein accumulation in different tissues and organs of chickpea seedlings and plants and its subcellular localization, which could indicate the possible function of ST1. The raising of specific antibodies against ST1 protein revealed that its accumulation in epicotyls and radicles was related to their elongation rate. Its pattern of tissue location in cotyledons during seed formation and early seed germination, as well as its localization in the perivascular fibres of epicotyls and radicles, indicated a possible involvement in seed germination and seedling growth. ST1 protein appears both inside the cell and in the cell wall. This double subcellular localization was found in every organ in which the ST1 protein was detected: seeds, cotyledons and seedling epicotyls and radicles.

Improved protein quality in transgenic soybean expressing a de novo synthetic protein, MB-16

To improve soybean [Glycine max (L.) Merrill] seed nutritional quality, a synthetic gene, MB-16 was introduced into the soybean genome to boost seed methionine content. MB-16, an 11 kDa de novo protein enriched in the essential amino acids (EAAs) methionine, threonine, lysine and leucine, was originally developed for expression in rumen bacteria. For efficient seed expression, constructs were designed using the soybean codon bias, with and without the KDEL ER retention sequence, and β-conglycinin or cruciferin seed specific protein storage promoters. Homozygous lines, with single locus integrations, were identified for several transgenic events. Transgene transmission and MB-16 protein expression were confirmed to the T5 and T7 generations, respectively. Quantitative RT-PCR analysis of developing seed showed that the transcript peaked in growing seed, 5-6 mm long, remained at this peak level to the full-sized green seed and then was significantly reduced in maturing yellow seed. Transformed events carrying constructs with the rumen bacteria codon preference showed the same transcription pattern as those with the soybean codon preference, but the transcript levels were lower at each developmental stage. MB-16 protein levels, as determined by immunoblots, were highest in full-sized green seed but the protein virtually disappeared in mature seed. However, amino acid analysis of mature seed, in the best transgenic line, showed a significant increase of 16.2 and 65.9 % in methionine and cysteine, respectively, as compared to the parent. This indicates that MB-16 elevated the sulfur amino acids, improved the EAA seed profile and confirms that a de novo synthetic gene can enhance the nutritional quality of soybean.

Soybean seed proteome rebalancing

The soybean seed's protein content and composition are regulated by both genetics and physiology. Overt seed protein content is specified by the genotype's genetic framework and is selectable as a breeding trait. Within the genotype-specified protein content phenotype soybeans have the capacity to rebalance protein composition to create differing proteomes. Soybeans possess a relatively standardized proteome, but mutation or targeted engineering can induce large-scale proteome rebalancing. Proteome rebalancing shows that the output traits of seed content and composition result from two major types of regulation: genotype and post-transcriptional control of the proteome composition. Understanding the underlying mechanisms that specifies the seed proteome can enable engineering new phenotypes for the production of a high-quality plant protein source for food, feed, and industrial proteins.

Identification and roles of proteins for seed development in mungbean (Vigna radiata L.) seed proteomes

Proteomic analysis of developing mungbean (Vigna radiata L.) seeds has not yet been investigated in detail. Fifty-seven proteins were separated by 2-DE, identified by nanoelectrospray mass spectrometry from the present protein databases, and categorized according to their functions. Many of the identified enzymes were involved in central carbon metabolism; thus, a pathway illustrating starch synthesis/breakdown, sugar conversion for glycolysis, and tricarboxylic acid (TCA) cycle was proposed. Quantitative comparison of the protein expression revealed that during developmental process (11-21 days after flowering, DAF), proteins involved in glycolysis, TCA cycle, and alcoholic fermentation showed a trend to be down-regulated, whereas storage proteins were generally up-regulated. The downward tendency of central carbon metabolic proteins suggests a reduction in ATP and oxygen consumption associated with accumulation of storage compounds. UDP-glucose-1-pyrophosphorylase, an upstream enzyme in the starch ADP-Glc pathway, was found as a stably expressed protein throughout the growth stage, demonstrating its importance in mungbean starch biosynthesis. The temporal expression of metabolic enzymes suggests the coordination of an acclimation mechanism and cellular processes associated with accumulation of storage compounds in seed development.

RNAi trigger fragment truncation attenuates soybean FAD2-1 transcript suppression and yields intermediate oil phenotypes

Suppression of the microsomal ω6 oleate desaturase during the seed development of soybean (Glycine max) with the 420-bp soybean FAD2-1A intron as RNAi trigger shifts the conventional fatty acid composition of soybean oil from 20% oleic and 60% polyunsaturates to one containing greater than 80% oleic acid and less than 10% polyunsaturates. To determine whether RNAi could be attenuated by reducing the trigger fragment length, transgenic plants were generated to express successively shorter 5' or 3' deletion derivatives of the FAD2-1A intron. We observed a gradual reduction in transcript suppression with shorter trigger fragments. Fatty acid composition was less affected with shorter triggers, and triggers less than 60 bp had no phenotypic effect. No trigger sequences conferring significantly higher or lower suppression efficiencies were found, and the primary determinant of suppression effect was sequence length. The observed relationship of transcript suppression with the induced fatty acid phenotype indicates that RNAi is a saturation process and not a step change between suppressed and nonsuppressed states and intermediate suppression states can be achieved.

Silencing of soybean seed storage proteins results in a rebalanced protein composition preserving seed protein content without major collateral changes in the metabolome and transcriptome

The ontogeny of seed structure and the accumulation of seed storage substances is the result of a determinant genetic program. Using RNA interference, the synthesis of soybean (Glycine max) glycinin and conglycinin storage proteins has been suppressed. The storage protein knockdown (SP-) seeds are overtly identical to the wild type, maturing to similar size and weight, and in developmental ontogeny. The SP- seeds rebalance the proteome, maintaining wild-type levels of protein and storage triglycerides. The SP- soybeans were evaluated with systems biology techniques of proteomics, metabolomics, and transcriptomics using both microarray and next-generation sequencing transcript sequencing (RNA-Seq). Proteomic analysis shows that rebalancing of protein content largely results from the selective increase in the accumulation of only a few proteins. The rebalancing of protein composition occurs with small alterations to the seed's transcriptome and metabolome. The selectivity of the rebalancing was further tested by introgressing into the SP- line a green fluorescent protein (GFP) glycinin allele mimic and quantifying the resulting accumulation of GFP. The GFP accumulation was similar to the parental GFP-expressing line, showing that the GFP glycinin gene mimic does not participate in proteome rebalancing. The results show that soybeans make large adjustments to the proteome during seed filling and compensate for the shortage of major proteins with the increased selective accumulation of other proteins that maintains a normal protein content.

Transcription profiling of fertilization and early seed development events in a solanaceous species using a 7.7 K cDNA microarray from Solanum chacoense ovules

BACKGROUND

To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses.

RESULTS

We analyzed gene expression during S. chacoense embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (>or= +/- 2 fold change, p value <or= 0.01) in fertilized ovules compared to unfertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with the vast majority of the fertilization-regulated genes specifically or predominantly expressed in ovules (955 genes). During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development.

CONCLUSION

Our analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time point allowed the identification of a subset of stage-specific and transition-specific genes.

Plant embryogenesis: zygote to seed

Most differentiation events in higher plants occur continuously in the postembryonic adult phase of the life cycle. Embryogenesis in plants, therefore, is concerned primarily with establishing the basic shoot-root body pattern of the plant and accumulating food reserves that will be used by the germinating seedling after a period of embryonic dormancy within the seed. Recent genetics studies in Arabidopsis have identified genes that provide new insight into how embryos form during plant development. These studies, and others using molecular approaches, are beginning to reveal the underlying processes that control plant embryogenesis.

Cellular localization of soybean storage protein mRNA in transformed tobacco seeds

We transformed tobacco plants with a soybean beta-conglycinin gene that encodes the 1.7-kilobase beta-subunit mRNA. We showed that the beta-conglycinin mRNA accumulates and decays during tobacco seed development and that beta-conglycinin mRNA is undetectable in the tobacco leaf. We utilized in situ hybridization to localize beta-conglycinin mRNA within the tobacco seed. beta-Conglycinin mRNA is not detectable within the endosperm but is localized within specific embryonic cell types. The highest concentration of beta-conglycinin mRNA is found in cotyledon storage parenchyma cells. We conclude that sequences required for embryo expression, temporal control, and cell specificity are linked to the beta-conglycinin gene, and that factors regulating beta-conglycinin gene expression are compartmentalized within analogous soybean and tobacco seed regions.

An intron sense suppression construct targeting soybean FAD2-1 requires a double-stranded RNA-producing inverted repeat T-DNA insert

We demonstrate that the transformation of soybean (Glycine max) with sense suppression constructs using intron sequences from the fatty acid oleyl Delta12 desaturase gene FAD2-1A leads to efficient and specific reduction of FAD2-1 transcripts in developing seeds, increased oleic acid, and decreased polyunsaturated fatty acids. The related FAD2-2 transcripts are only marginally affected. Despite screening a large number of independent transformants, no single-copy efficacious transformants could be found. Invariably, all the least complex transgenic loci have two T-DNA copies in an inverted repeat configuration, centered at the right borders. We show that this T-DNA configuration produces an inverted repeat transcript and that small interfering RNAs accumulate against the target sequence.

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors

Most of the transcription factors (TFs) responsible for controlling seed development are not yet known. To identify TF genes expressed at specific stages of seed development, including those unique to seeds, we used Affymetrix GeneChips to profile Arabidopsis genes active in seeds from fertilization through maturation and at other times of the plant life cycle. Seed gene sets were compared with those expressed in prefertilization ovules, germinating seedlings, and leaves, roots, stems, and floral buds of the mature plant. Most genes active in seeds are shared by all stages of seed development, although significant quantitative changes in gene activity occur. Each stage of seed development has a small gene set that is either specific at the level of the GeneChip or up-regulated with respect to genes active at other stages, including those that encode TFs. We identified 289 seed-specific genes, including 48 that encode TFs. Seven of the seed-specific TF genes are known regulators of seed development and include the LEAFY COTYLEDON (LEC) genes LEC1, LEC1-LIKE, LEC2, and FUS3. The rest represent different classes of TFs with unknown roles in seed development. Promoter-beta-glucuronidase (GUS) fusion experiments and seed mRNA localization GeneChip datasets showed that the seed-specific TF genes are active in different compartments and tissues of the seed at unique times of development. Collectively, these seed-specific TF genes should facilitate the identification of regulatory networks that are important for programming seed development.

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

BACKGROUND

The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content.

RESULTS

A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix Soy GeneChip and high-throughput Illumina whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region.

CONCLUSIONS

This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.

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.

Spatial and temporal control of transcription of the soybean beta-conglycinin alpha subunit gene is conferred by its proximal promoter region and accounts for the unequal distribution of the protein during embryogenesis

Differentiation into specific embryo cell types correlates with the processes that lead to the accumulation of seed storage proteins in plants. The alpha subunit of beta-conglycinin, a major component of seed storage proteins in soybean, accumulates at a higher level in cotyledons than in the embryonic axis in developing embryos. To understand the mechanisms underlying this phenomenon, we characterized the upstream region of the alpha subunit gene in terms of transcriptional control using transgenic Arabidopsis thaliana plants carrying reporter gene constructs comprising the 1357-bp upstream sequence of the alpha subunit gene and the beta-glucuronidase (GUS) gene. Analysis of the time-course-dependent pattern of GUS expression revealed that the expression was first confined to the cotyledons and occurred later in the entire embryo during embryogenesis. The level of GUS expression was higher in cotyledons than in the embryonic axis throughout the period of its expression, coincident with the distribution of the alpha subunit protein in soybean embryos. By testing progressively shorter promoter fragments, the cis-acting elements responsible for transcriptional activation in the cotyledons and the embryonic axis were both localized to the region spanning -245 to -161 relative to the transcription start site. It is also concluded that the upstream region up to -245 is sufficient to control the spatial and temporal pattern of transcription, while further upstream regions influence transcription rate without affecting the transcriptional pattern. Overall, these results indicate that the unequal distribution of alpha subunit protein within the embryos is established primarily as a consequence of differential transcriptional activation controlled by a short proximal promoter region of the gene in different embryonic tissues.

Transcriptional regulation of storage protein synthesis during dicotyledon seed filling

Seeds represent a major source of nutrients for human and animal livestock diets. The nutritive value of seeds is largely due to storage products which accumulate during a key phase of seed development, seed filling. In recent years, our understanding of the mechanisms regulating seed filling has advanced significantly due to the diversity of experimental approaches used. This review summarizes recent findings related to transcription factors that regulate seed storage protein accumulation. A framework for the regulation of storage protein synthesis is established which incorporates the events before, during and after seed storage protein synthesis. The transcriptional control of storage protein synthesis is accompanied by physiological and environmental controls, notably through the action of plant hormones and other intermediary metabolites. Finally, recent post-genomics analyses on different model plants have established the existence of a conserved seed filling process involving the master regulators (LEC1, LEC2, ABI3 and FUS3) but also revealed certain differences in fine regulation between plant families.

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.

Molecular cloning, sequence characterization and tissue-specific expression of six NAC-like genes in soybean (Glycine max (L.) Merr.)

NAC proteins have been considered as one of the novel classes of plant-specific transcription factors functioning in diverse and vital physiological processes during plant development. In this study, six NAC-like genes from soybean, designated as GmNAC1-GmNAC6, were cloned and characterized. They each contained two introns and three exons and shared conservative structure of genomic organization. The predicted proteins, GmNAC1-GmNAC6, were similar in sequences, especially in NAC domain regions. However, RT-PCR analysis indicated that each GmNAC gene exhibited a specific expression pattern in tissues examined. GmNAC2, 3, 4, and 6 were expressed in most tested tissues while GmNAC1 and GmNAC5 were limited to a few tissues. In addition, expression patterns of GmNAC genes were characterized during seed filling and coordinated expression was observed between GmNAC genes. Finally, based on phylogenetic analysis, six GmNAC proteins were classed into five subgroups with different putative functions. To our knowledge, this is the first report on molecular cloning and initial characterization of NAC-like genes in soybean. Our results may provide the basis for future investigations of NAC-like genes' roles in seed development and other physiological processes in this important crop.

A novel cis-acting element, ESP, contributes to high-level endosperm-specific expression in an oat globulin promoter

To examine the genetic controls of endosperm (ES) specificity, several cereal seed storage protein (SSP) promoters were isolated and studied using a transient expression analysis system. An oat globulin promoter (AsGlo1) capable of driving strong ES-specific expression in barley and wheat was identified. Progressive 5' deletions and cis element mutations demonstrated that the mechanism of specificity in the AsGlo1 promoter was distinct from that observed in glutelin and prolamin promoters. A novel interrupted palindromic sequence, ACATGTCATCATGT, was required for ES specificity and substantially contributed to expression strength of the AsGlo1 promoter. This sequence was termed the endosperm specificity palindrome (ESP) element. The GCN4 element, which has previously been shown to be required for ES specificity in cereal SSP promoters, had a quantitative role but was not required for tissue specificity. The 960-bp AsGlo1 promoter and a 251-bp deletion containing the ESP element also drove ES-specific expression in stably transformed barley. Reporter gene protein accumulated at very high levels (10% of total soluble protein) in ES tissues of plants transformed with an AsGlo1:GFP construct. Expression strength and tissue specificity were maintained over five transgenic generations. These attributes make the AsGlo1 promoter an ideal promoter for biotechnology applications. In conjunction with previous findings, our data demonstrate that there is more than one genetically distinct mechanism by which ES specificity can be achieved in cereal SSP promoters, and also suggest that there is redundancy between transcriptional and post-transcriptional tissue specificity mechanisms in cereal globulin genes.

Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean

Globular somatic embryos can be induced from immature cotyledons of soybean (Glycine max L. Merr. cv Jack) placed on high levels of the auxin 2,4-dichlorophenoxyacetic acid (2,4-D). Somatic embryos develop from the adaxial side of the cotyledon, whereas the abaxial side evolves into a callus. Using a 9,280-cDNA clone array, we have compared steady-state RNA from the adaxial side from which embryos develop and from the abaxial callus at five time points over the course of the 4 weeks necessary for the development of globular embryos. In a second set of experiments, we have profiled the expression of each clone in the adaxial side during the same period. A total of 495 genes differentially expressed in at least one of these experiments were grouped according to the similarity of their expression profiles using a nonhierarchical clustering algorithm. Our results indicate that the appearance of somatic embryos is preceded by dedifferentiation of the cotyledon during the first 2 weeks on auxin. Changes in mRNA abundance of genes characteristic of oxidative stress and genes indicative of cell division in the adaxial side of the cotyledons suggest that the arrangement of the new cells into organized structures might depend on a genetically controlled balance between cell proliferation and cell death. Our data also suggest that the formation of somatic globular embryos is accompanied by the transcription of storage proteins and the synthesis of gibberellic acid.

Cosuppression of the alpha subunits of beta-conglycinin in transgenic soybean seeds induces the formation of endoplasmic reticulum-derived protein bodies

The expression of the alpha and alpha' subunits of beta-conglycinin was suppressed by sequence-mediated gene silencing in transgenic soybean seed. The resulting seeds had similar total oil and protein content and ratio compared with the parent line. The decrease in beta-conglycinin protein was apparently compensated by an increased accumulation of glycinin. In addition, proglycinin, the precursor of glycinin, was detected as a prominent polypeptide band in the protein profile of the transgenic seed extract. Electron microscopic analysis and immunocytochemistry of maturing transgenic soybean seeds indicated that the process of storage protein accumulation was altered in the transgenic line. In normal soybeans, the storage proteins are deposited in pre-existing vacuoles by Golgi-derived vesicles. In contrast, in transgenic seed with reduced beta-conglycinin levels, endoplasmic reticulum (ER)-derived vesicles were observed that resembled precursor accumulating-vesicles of pumpkin seeds and the protein bodies accumulated by cereal seeds. Their ER-derived membrane of the novel vesicles did not contain the protein storage vacuole tonoplast-specific protein alpha-TIP, and the sequestered polypeptides did not contain complex glycans, indicating a preGolgi and nonvacuolar nature. Glycinin was identified as a major component of these novel protein bodies and its diversion from normal storage protein trafficking appears to be related to the proglycinin buildup in the transgenic seed. The stable accumulation of proteins in a protein body compartment instead of vacuolar accumulation of proteins may provide an alternative intracellular site to sequester proteins when soybeans are used as protein factories.

Characterization of a soybean

Kunitz trypsin inhibitor, an abundant soybean [Glycine max (L.) Merr.] seed protein, has a molecular mass of 21500 Da and is specific for serine proteases. A soybean mutant (P.I. 196168) was characterized to determine the molecular basis for reduced Kunitz trypsin inhibitor levels during seed development. Western blot analysis revealed that P.I. 196168, in comparison to Amsoy 71, accumulated low amounts of Kunitz trypsin inhibitor protein. Non-denaturing polyacrylamide enzyme activity gels indicated that Amsoy 71 seeds contained at least five distinct zones of trypsin inhibitor activity. However, P.I. 196168 contained only four zones of enzyme inhibition. The coding region of the most abundant trypsin inhibitor gene (KTi3) was isolated from Amsoy 71 and P.I. 196168 by PCR. DNA sequence comparisons of the Kunitz trypsin inhibitor coding regions revealed two deletions and one G to T transversion have occurred. These mutations introduced four stop codons in the reading frame, resulting in a truncated protein. Northern blot analysis revealed that P.I. 196168 accumulated drastically lower amounts of KTi3 mRNA when compared with Amsoy 71.

Auxin and brassinosteroid differentially regulate the expression of three members of the 1-aminocyclopropane-1-carboxylate synthase gene family in mung bean (Vigna radiata L.)

Indole-3-acetic acid (IAA) markedly increased ethylene production by inducing the expression of three 1aminocyclopropane-1-carboxylate (ACC) synthase cDNAs (pVR-ACS1, pVR-ACS6 and pVR-ACS7) in mung bean hypocotyls. Results from nuclear run-on transcription assay and RNA gel blot studies revealed that all three genes were transcriptionally active displaying unique patterns of induction by IAA and various hormones in etiolated hypocotyls. Particularly, 24-epibrassinolide (BR), an active brassinosteroid, specifically enhanced the expression of VR-ACS7 by a distinct temporal induction mechanism compared to that of IAA. In addition, BR synergistically increased the IAA-induced VR-ACS6 and VR-ACS7 transcript levels, while it effectively abolished both the IAA- and kinetin-induced accumulation of VR-ACS1 mRNA. In light-grown plants, VR-ACS1 was induced by IAA in roots, and VR-ACS6 in epicotyls. IAA- and BR-treatments were not able to increase the VR-ACS7 transcript in the light-grown tissues. These results indicate that the expression of ACC synthase multigene family is regulated by complex hormonal and developmental networks in a gene- and tissue-specific manner in mung bean plants. The VR-ACS7 gene was isolated, and chimeric fusion between the 2.4 kb 5'-upstream region and the beta-glucuronidase (GUS) reporter gene was constructed and introduced into Nicotiana tabacum. Analysis of transgenic tobacco plants revealed the VR-ACS7 promoter-driven GUS activity at a highly localized region of the hypocotyl-root junction of control seedlings, while a marked induction of GUS activity was detected only in the hypocotyl region of the IAA-treated transgenic seedlings where rapid cell elongation occurs. Although there was a modest synergistic effect of BR on the IAA-induced GUS activity, BR alone failed to increase the GUS activity, suggesting that induction of VR-ACS7 occurs via separate signaling pathways in response to IAA and BR. A scheme of the multiple regulatory pathways for the expression of ACC synthase multigene family by auxin and BR is presented.

Induction of a beta-phaseolin promoter by exogenous abscisic acid in tobacco: developmental regulation and modulation by external sucrose and Ca2+ ions

Phaseolin genes are induced by unidentified factors at the onset of seed maturation in embryos of both Phaseolus and tobacco. We show that in tobacco, expression of a beta-phaseolin promoter-GUS (PHSbeta-uidA) mRNA and the corresponding GUS activity, could be induced by abscisic acid (ABA). The effect paralleled an increase in the amount of endogenous 12S globulin (Glb12S) mRNA. In contrast, ABA repressed the expression of isocitrate lyase (ll9) mRNA. The responses of PHSbeta-uidA and Glb12S to ABA declined markedly between 11 and 13 DAF, indicating that they are developmentally regulated. We also show evidence that the ABA response of PHSbeta-uidA can be modulated by the external concentrations of sucrose and Ca2+ ion. These compounds inhibited the response if added to the medium separately, in the concentration ranges of 80-200 mM for sucrose and 0.76-20 mM for CaCl2. However, the presence of both sucrose and CaCl2 restored the ABA response to 20-40% of the maximum value measured in sucrose- and CaCl2-free media. These results suggest that ABA induction of beta-phaseolin gene expression is modulated by developmental signals and by the external supply of sucrose and calcium to the embryos.

The RY sequence is necessary but not sufficient for the transcription activation of a winged bean chymotrypsin inhibitor gene in developing seeds

A winged bean Kunitz-type chymotrypsin inhibitor (WCI) is expressed in seeds and tuberous roots. In seeds, the expression of WCI is restricted to the period between the mid- and late-maturation stage. To understand the mechanisms that regulate the expression of WCI genes, we analyzed the promoter activity of the upstream region of the WCI-3b gene, which encodes a major WCI protein, in transgenic tobacco plants. By using a series of constructs with 5' deletions in the upstream sequences, the region between -882 and -623, relative to the transcription start site, was shown to contain multiple sequences which are responsible for high level expression in mid-maturation stage seeds. However, when this region was fused to the cauliflower mosaic virus 35S core promoter in both orientations, the chimeric promoters showed only a weak transcription activity in transgenic tobacco plants. Further analyses using internal deletion constructs revealed that the region between -882 and -174 is required for the transcription activation. Disruption of the RY sequence at -517, which is conserved in many seed protein genes, resulted in a drastic reduction of the transcription activity in seeds. These results suggest that sequences necessary for high level induction of the WCI-3b gene transcription in developing seeds are dispersed in the region between -882 and -174, and that the RY sequence is one of these sequences.

The upstream domain of soybean oleosin genes contains regulatory elements similar to those of legume storage proteins

Seed reserve storage products consisting of proteins, oil and starch are accumulated in a developmentally coordinated pattern. The control of the vacuolar storage protein expression has been shown to be transcriptionally regulated and involves a series of positive and negative regulatory as well as enhancing gene elements. We have analyzed the upstream sequence of the genes encoding the soybean oleosins, the protein that encases the oil body. We have found that soybean oleosin genes possess regulatory elements in upstream domain that are similar to those found in vacuolar storage protein genes.

Differential expression of genes during legume seed development

The accumulation of certain proteins specific to those tissues in the developing seeds of legumes represents a system of academic and practical significance in the study of differential gene expression. Besides the simple distinction between ‘seed-specific’ and ‘non-seed-specific’ expression of genes, further controls are present in determining the level of expression of a particular gene, and the variations in its expression with cell type, developmental stage and environmental perturbation. There are also genetic factors that lead to variations in the expression of homologous genes between lines or species. Gene expression can be assayed at the levels of synthesis of specific proteins, level of mRNA species, and transcription of specific genes, and the results of all these assays lead to a broad correlation between events at the level of the gene and protein deposition in the developing seed. This correlation is strong at earlier stages of seed development, but is weaker at later stages. Evidence is presented that control of gene expression occurs both at transcription and by post-transcriptional processes. Seed protein genes have conserved sequences in their 5' flanking regions that are specific to gene families, and these are suggested to be involved in transcriptional control of the expression of these genes. Although such sequences are unlikely to be solely responsible for transcription control, there is no strong evidence for changes in DNA methylation or in chromatin conformation being causally related to expression of seed protein genes. Control of gene expression in developing seeds is considered in terms of a genetically determined, conserved developmental programme, the aim of which is to produce a viable embryo. This programme will allow considerable plasticity in gene expression within constraints prescribed by seed viability. Although it may be possible to understand the immediate controls of seed protein gene expression, present systems are not adequate to study the genes that control the developmental programme. More fundamental investigations will be assisted by mutants that possess altered seed development patterns.

Regulation of plant gene expression

Differential gene expression is required to establish and maintain specific developmental states in higher plants. For example, an anther has at least 11000 diverse mRNAs that are absent from the polysomes of other organ systems, and the root has at least 7000 organ-specific mRNAs. Both transcriptional and post-transcriptional processes regulate the sequence composition and prevalence distribution of each developmental-specific mRNA set. Soybean seed protein genes represent an excellent example of a highly regulated gene set. These genes are temporally and spatially regulated during embryogenesis, and are either inactive or expressed at low levels in mature plant organ systems. Gene transfer experiments indicate that soybean seed protein genes retain their developmental-specific expression programme in transformed tobacco plants. In addition, large polygenic clusters can be transferred from soybean to tobacco, and the expression pattern of each gene within the cluster is maintained in the foreign cell environment. Although the DNA sequences and cellular factors required to control seed protein gene expression are not yet known, gene transfer studies and emerging DNA binding protein technology should facilitate their identification in the near future.

Isolation and characterization of a diverse set of genes from carrot somatic embryos

The early events in plant embryogenesis are critical for pattern formation, since it is during this process that the primary apical meristems and the embryo polarity axis are established. However, little is known about the molecular events that are unique to the early stages of embryogenesis. This study of gene expression during plant embryogenesis is focused on identifying molecular markers from carrot (Daucus carota) somatic embryos and characterizing the expression and regulation of these genes through embryo development. A cDNA library, prepared from polysomal mRNA of globular embryos, was screened using a subtracted probe; 49 clones were isolated and preliminarily characterized. Sequence analysis revealed a large set of genes, including many new genes, that are expressed in a variety of patterns during embryogenesis and may be regulated by different molecular mechanisms. To our knowledge, this group of clones represents the largest collection of embryo-enhanced genes isolated thus far, and demonstrates the utility of the subtracted-probe approach to the somatic embryo system. It is anticipated that many of these genes may serve as useful molecular markers for early embryo development.

Differential stability of zein mRNA in developing corn kernel

The lifetime of the zein mRNA in a developing corn (Zea mays L.) kernel under genome transcription blockade with actinomycin D (in vivo) and in a cell-free system (in vitro) was studied. After a 10 h blockade of gene transcription with actinomycin D, only 55% of 19 kDa zein mRNA and 40% of 22 kDa mRNA were detected in a developing kernel of normal corn. In that of the opaque-2 mutant 80% of 19 kDa zein mRNA remained. To examine the relative stability of poly(A)-containing mRNA, cell-free systems from rabbit reticulocyte lysate and wheat-germ extract were used. In both cases only 40% of 19 kDa zein mRNA and 60% of 22 kDa zein mRNA decayed during a 30 min incubation. Differential mRNA degradation of poly(A)-containing zein mRNA was observed on affinity chromatography; poly(A)-containing 19 kDa zein mRNA from normal corn partially decayed by elution from poly(U)-Sepharose whereas that from opaque-2 remained stable. These data suggest that differential mRNA stability is an important factor in the regulation of the zein gene expression in a developing corn kernel.

Transcriptional and Posttranscriptional Regulation of Dormancy-Associated Gene Expression by Afterripening in Wild Oat

To investigate whether the afterripening-induced changes in gene expression are at the transcriptional or posttranscriptional level in wild oat (Avena fatua) seeds, we chose four dormancy-associated genes to estimate their relative transcription activities and the stability of their corresponding transcripts in afterripened and dormant embryos. The transcription activities for those genes were 1.5 to 7 times higher in dormant embryos than in afterripened embryos 24 h after incubation, as determined by nuclear run-on assays. The half-lives of the transcripts in afterripened and dormant embryos were estimated by the use of actinomycin D. The application of actinomycin D resulted in the stabilization of the transcripts. Nevertheless, the results indicated that the half-lives of the transcripts were much greater in dormant embryos than in afterripened embryos. Considering the great differences in the steady-state levels and the half-lives of the mRNAs, and the relatively small differences in transcription activities of the genes between afterripened and dormant embryos, we conclude that afterripening regulates the expression of dormancy-associated genes in excised embryos mainly at the posttranscriptional level and that transcriptional control plays a minor role.

The starch phosphorylase gene is subjected to different modes of regulation in starch-containing tissues of potato

Analysis of the levels of starch phosphorylase mRNA and its product in the various organs of the potato plant indicates that the gene is differentially regulated, leading to a high accumulation of the gene product in tubers. The amount of phosphorylase transcripts synthesized in nuclei isolated from tubers and leaves indicates that the difference in the steady-state levels of phosphorylase mRNA in these organs can be explained by different rates of initiation of transcription. However, while rates of initiation of transcription are similar in tubers and stems, the steady-state level of phosphorylase mRNA is much lower in the stem. Transgenic potato plants expressing the beta-glucuronidase (GUS) gene under the control of 5'-flanking sequences of the phosphorylase gene exhibited high levels of GUS activity in petioles, stems, stolons, tubers and roots, but low levels in leaves. This confirms the results of transcription assays observed for leaves, stems and tubers, and indicates that accumulation of phosphorylase mRNA in stems and tubers is not controlled solely by transcription initiation. Finally, histochemical analysis for GUS activity in transgenic potato plants suggests that transcription of the phosphorylase gene predominantly occurs in starch-containing cells associated to vascular tissues, and suggests a role for starch phosphorylase in the mobilization of starch stored along the translocation pathway.

The regulator of MAT2 (ROM2) protein binds to early maturation promoters and represses PvALF-activated transcription

The regulation of maturation (MAT)- and late embryogenesis (LEA)-specific gene expression in dicots involves factors related to ABI3, a seed-specific component of the abscisic acid signal transduction pathways from Arabidopsis. In French bean (Phaseolus vulgaris), the ABI3-like factor, PvALF, activates transcription from MAT promoters of phytohemagglutinin (DLEC2) and beta-phaseolin (PHS beta) genes. We describe the regulator of MAT2 (ROM2) as a basic leucine zipper (bZIP) DNA binding protein that recognizes motifs with symmetric (ACGT) and asymmetric (ACCT) core elements present in both MAT promoters. ROM2 antagonizes trans-activation of the DLEC2 promoter by PvALF in transient expression assays. Repression was abolished by mutations that prevented binding of ROM2 to the DLEC2 seed enhancer region. Moreover, a hybrid protein composed of a PvALF activation domain and the DNA binding and dimerization domain of ROM2 activated gene expression, indicating that ROM2 recognizes the DLEC2 enhancer in vivo; consequently, ROM2 functions as a DNA binding site-dependent repressor. Supershift analysis of nuclear proteins, using a ROM2-specific antibody, revealed an increase in ROM2 DNA binding activity during seed desiccation. A corresponding increase in ROM2 mRNA coincided with the period when DLEC2 mRNA levels declined in embryos. These results demonstrate developmental regulation of the ROM2 repressor and point to a role for this factor in silencing DLEC2 transcription during late embryogenesis.

Abundance and half-life of the distinct oat phytochrome A3 and A4 mRNAs

Gene-preferential oligonucleotide probes were used to determined the relative abundance and half-lives of distinct oat phytochrome A (PHYA) mRNAs. Oat PHYA mRNAs are highly conserved in the 5'-untranslated region and the coding region, but the 3'-untranslated region has an overall lower sequence conservation and was the source of gene-preferential probes. PHYA3 mRNA was estimated to be ca. 61% of the oat PHYA mRNA pool present in poly(A)+ RNA from dark-grown seedlings. The half-lives for PHYA3 and PHYA4 mRNAs were both estimated to be ca. 30 min, and a similar short half-life was estimated for the average PHYA mRNA. Sequence comparisons of PHYA mRNAs from four grass species identified conserved sequences within the 5'- and 3'-untranslated regions that might be important for PHYA mRNA degradation.

Transgenic analysis of a hybrid poplar wound-inducible promoter reveals developmental patterns of expression similar to that of storage protein genes

The wound-inducible win3 multigene family from hybrid poplars (Populus trichocarpa x Populus deltoides) encodes proteins with structural similarities with Kunitz-type protease inhibitors (H.D. Bradshaw Jr., J.B. Hollick, T.J. Parsons, H.R.G. Clarke, M.P. Gordon [1990] Plant Mol Biol 14: 51-59), and at least one member, win3.12, is transcribed de novo in the injured and uninjured leaves of wounded trees (J.B. Hollick, M.P. Gordon [1993] Plant Mol Biol 22: 561-572). A previous study demonstrated that 1352 bp of 5' flanking DNA from the win3.12 gene confers local wound-regulated expression of the beta-glucuronidase gene in transgenic tobacco (Nicotiana tabacum cv Xanthi n.c.) (J.B. Hollick, M.P. Gordon [1993] Plant Mol Biol 22: 561-572). We extend this transgenic analysis here by examining the developmental regulation and systemic wound induction conferred by the same transgene construct in tobacco. Biochemical and histochemical surveys of beta-glucuronidase activity are described for four, independent transgenic lines. The observed spatial and temporal expression patterns coincide with dormant storage tissues and with previously described expression patterns for both seed and vegetative storage protein genes. Developmental northern blot analysis of win3 RNA levels in poplar seeds confirms that proper temporal expression of the reporter gene is maintained during tobacco seed maturation. These results demonstrate that a putative Kunitz-type protease inhibitor can be wound inducible in addition to being expressed in developing seeds.

Positive and negative cis-regulatory regions in the soybean glycinin promoter identified by quantitative transient gene expression

The 5' and 3' flanking regions of the soybean glycinin gene, Gy1, responsible for expression in seeds, were analyzed by quantitative transient expression assay. The construct containing the β-glucuronidase (uidA) reporter gene under the control of the 1.12 kb Gy1 promoter and 0.74 kb Gy1 terminator was introduced into immature soybean seeds and leaves by particle bombardment. To normalize the variability of introduction efficiency, a second reporter gene, firefly luciferase, was cobombarded as an internal standard, and relative activities (GUS/luciferase) were measured. There was a seed-specific β-glucuronidase (GUS) expression, as observed by X-Gluc staining. Compared with the nopaline synthase gene (nos) terminator, the Gy1 terminator enhanced the level of expression in immature seeds, indicating that the terminator region of the glycinin gene is involved in the activation of the gene expression in these seeds. To identify cis-regulatory elements in the glycinin gene upstream sequence, deleted derivatives of the promoter were fused to the luciferase reporter gene. The expression could be measured with a higher accuracy, and constructs were introduced with the internal reporter uidA gene into immature seeds. The results suggest the presence of a positive regulatory element in the -620 to --380 region of the Gy1 promoter. A deletion which eliminates the legumin box with its RY element led to increased relative activity, suggesting that this box is negatively regulating expression of the seed storage protein gene. Analysis of mutant promoters also suggest that the RY element involves negative regulation in seeds. This quantitative transient expression assay using particle bombardment provides a reliable system for the study of seed-specific gene expression in soybeans.

Organ-Specific Stability of Two Lemna rbcS mRNAs Is Determined Primarily in the Nuclear Compartment

It has previously been shown that the organ-specific expression of two members of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene family is post-transcriptionally regulated in Lemna gibba. While both small subunit genes encoding SSU1 and SSU5B were transcribed at comparable levels in root and frond nuclei, SSU1 mRNA accumulated to high levels in both roots and fronds in contrast to SSU5B mRNA, which was of very low abundance in the roots compared with the fronds. In this study, we have used two approaches to pinpoint the step(s) at which SSU1 and SSU5B mRNAs are differentially accumulated in these organs. In the first approach, total nuclear steady state mRNA was isolated from roots and fronds, and the amount of each transcript was measured by RNase protection assays and compared with the transcription rates in isolated nuclei. In the second approach, cordycepin was used to inhibit mRNA synthesis in Lemna fronds or roots, and the rate of decay of each mRNA was measured by RNA gel blot analysis or RNase protection assays. Our findings indicate that the differential accumulation of SSU1 and SSU5B mRNAs in the fronds versus the roots is determined primarily in the nuclear compartment. In addition, SSU1 was found to have a longer half-life in total steady state mRNA than SSU5B had in both organs. This feature probably accounts for SSU1 being the predominantly expressed family member.