Molecular cloning, genomic organization, expression and evolution of 12S seed storage protein genes of Arabidopsis thaliana

Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants

The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.

Linum usitatissimum ABI3 enhances the accumulation of seed storage reserves and tolerance to environmental stresses during seed germination and seedling establishment in Arabidopsis thaliana

Flax (Linum usitatissimum) is an important oil crop in arid and semi-arid regions of North and Northwest China, and its seeds are rich in nutritious storage reserves, such as polyunsaturated fatty acids (FAs) and proteins. However, the regulatory networks that control the accumulation of seed storage reserves in flax are still largely unknown. In this study, we found that LuABI3-1 and LuABI3-2 homologs from the flax cultivar 'Longya 10' play important roles in regulating the accumulation of seed storage reserves in Arabidopsis thaliana. The results of subcellular localization and transcriptional activity assays showed that both LuABI3-1 and LuABI3-2 function as transcription factors. Overexpression of either LuABI3-1 or LuABI3-2 resulted in the significant increase in the contents of total seed FAs and storage proteins, but did not alter other key agronomic traits in A. thaliana. Accordingly, the expression of key genes involved in the biosynthesis of FAs and storage proteins was also greatly up-regulated in the developing seeds of LuABI3-1-overexpression lines. Additionally, both LuABI3-1 and LuABI3-2 enhanced the tolerance to the high salt and mannitol stresses during seed germination and seedling establishment in A. thaliana. These results increase our understanding of the LuABI3 regulatory functions and provide promising targets for genetic manipulation of L. usitatissimum to innovate the germplasm resources and cultivate high yield and quality varieties.

The MADS-domain factor AGAMOUS-Like18 promotes somatic embryogenesis

AGAMOUS-Like 18 (AGL18) is a MADS domain transcription factor (TF) that is structurally related to AGL15. Here we show that, like AGL15, AGL18 can promote somatic embryogenesis (SE) when ectopically expressed in Arabidopsis (Arabidopsis thaliana). Based on loss-of-function mutants, AGL15 and AGL18 have redundant functions in developmental processes such as SE. To understand the nature of this redundancy, we undertook a number of studies to look at the interaction between these factors. We studied the genome-wide direct targets of AGL18 to characterize its roles at the molecular level using chromatin immunoprecipitation (ChIP)-SEQ combined with RNA-SEQ. The results demonstrated that AGL18 binds to thousands of sites in the genome. Comparison of ChIP-SEQ data for AGL15 and AGL18 revealed substantial numbers of genes bound by both AGL15 and AGL18, but there were also differences. Gene ontology analysis revealed that target genes were enriched for seed, embryo, and reproductive development as well as hormone and stress responses. The results also demonstrated that AGL15 and AGL18 interact in a complex regulatory loop, where AGL15 inhibited transcript accumulation of AGL18, while AGL18 increased AGL15 transcript accumulation. Co-immunoprecipitation revealed an interaction between AGL18 and AGL15 in somatic embryo tissue. The binding and expression analyses revealed a complex crosstalk and interactions among embryo TFs and their target genes. In addition, our study also revealed that phosphorylation of AGL18 and AGL15 was crucial for the promotion of SE.

Proteoform of Arabidopsis seed storage protein identified by functional proteomics approach exhibits acyl hydrolase activity during germination

Lipases play a crucial role in the life cycle of seed plants and the oil content of the seed is highly regulated by the lipase activity. Hence, understanding the role of lipases during germination and post-germination will provide insights into lipid mobilization. However, to date, no lipase gene has been identified in seeds except, Sugar-dependent-1 in Arabidopsis. Hence, in the present study, we employed a functional proteomic approach for the identification of seed-specific lipase. Activity-Based Proteome Profiling (ABPP) of Arabidopsis mature and germinating seeds revealed the expression of a functional serine hydrolase exclusively during germination. The mass-spectrometry analysis reveals the identity and amino acid sequence of the protein correspond to AT4G28520 gene, a canonical 12S Seed Storage Protein (SSP). Interestingly, the identified SSP was a proteoform of AT4G28520 (SL-AT4G28520) and exhibited >90% identity with the canonical AT4G28520 (FL-AT4G28520). Heterologous expression and enzyme assays indicated that SL-AT4G28520 protein indeed possesses monoacylglycerol lipase activity, while the FL-AT4G28520 protein didn't exhibit any detectable activity. Functional proteomics and lipidomics analysis demonstrated a catalytic function of this SSP. Collectively, this is the first report, which suggests that SL-AT4G28520 encodes a lipase, and the activity is depending on the physiological condition.

Similarities and Differences of Photosynthesis Establishment Related mRNAs and Novel lncRNAs in Early Seedlings (Coleoptile/Cotyledon vs. True Leaf) of Rice and Arabidopsis

Photosynthesis uses sunlight and carbon dioxide to produce biomass that is vital to all life on earth. In seed plants, leaf is the main organ for photosynthesis and production of organic nutrients. The seeds are mobilized to fuel post-germination seedling growth until seedling photosynthesis can be efficiently established. However, the photosynthesis and metabolism in the early growth and development have not been studied systematically and are still largely unknown. In this study, we used two model plants, rice (Oryza sativa L.; monocotyledonous) and Arabidopsis (Arabidopsis thaliana; dicotyledonous) to determine the similarities and differences in photosynthesis in cotyledons and true leaves during the early developmental stages. The photosynthesis-related genes and proteins, and chloroplast functions were determined through RNA-seq, real-time PCR, western blotting and chlorophyll fluorescence analysis. We found that in rice, the photosynthesis established gradually from coleoptile (cpt), incomplete leaf (icl) to first complete leaf (fcl); whereas, in Arabidopsis, photosynthesis well-developed in cotyledon, and the photosynthesis-related genes and proteins expressed comparably in cotyledon (cot), first true leaf (ftl) and second true leaf (stl). Additionally, we attempted to establish an mRNA-lncRNA signature to explore the similarities and differences in photosynthesis establishment between the two species, and found that DEGs, including encoding mRNAs and novel lncRNAs, related to photosynthesis in three stages have considerable differences between rice and Arabidopsis. Further GO and KEGG analysis systematically revealed the similarities and differences of expression styles of photosystem subunits and assembly factors, and starch and sucrose metabolisms between cotyledons and true leaves in the two species. Our results help to elucidate the gene functions of mRNA-lncRNA signatures.

Peptide transporter2 (PTR2) enhances water uptake during early seed germination in Arabidopsis thaliana

PTR2 in Arabidopsis thaliana is negatively regulated by ABI4 and plays a key role in water uptake by seeds, ensuring that imbibed seeds proceed to germination. Peptide transporters (PTRs) transport nitrogen-containing substrates in a proton-dependent manner. Among the six PTRs in Arabidopsis thaliana, the physiological role of the tonoplast-localized, seed embryo abundant PTR2 is unknown. In the present study, a molecular physiological analysis of PTR2 was conducted using ptr2 mutants and PTR2CO complementation lines. Compared with the wild type, the ptr2 mutant showed ca. 6 h delay in testa rupture and consequently endosperm rupture because of 17% lower water content and 10% higher free abscisic acid (ABA) content. Constitutive overexpression of the PTR2 gene under the control of the Cauliflower mosaic virus (CaMV) 35S promoter in ptr2 mutants rescued the mutant phenotypes. After cold stratification, a transient increase in ABA INSENSITIVE4 (ABI4) transcript levels during induction of testa rupture was followed by a similar increase in PTR2 transcript levels, which peaked prior to endosperm rupture. The PTR2 promoter region containing multiple CCAC motifs was recognized by ABI4 in electrophoretic mobility shift assays, and PTR2 expression was repressed by 67% in ABI4 overexpression lines compared with the wild type, suggesting that PTR2 is an immediate downstream target of ABI4. Taken together, the results suggest that ABI4-dependent temporal regulation of PTR2 expression may influence water status during seed germination to promote the post-germinative growth of imbibed seeds.

E3 SUMO ligase AtSIZ1 regulates the cruciferin content of Arabidopsis seeds

Arabidopsis thaliana E3 SUMO ligase SIZ1 (AtSIZ1) controls vegetative growth and development, including responses to nutrient deficiency and environmental stresses. Here, we analyzed the effect of AtSIZ1 and its E3 SUMO ligase activity on the amount of seed proteins. Proteomic analysis showed that the level of three major nutrient reservoir proteins, CRUCIFERIN1 (CRU1), CRU2, and CRU3, was reduced in the siz1-2 mutant compared with the wild type. However, quantitative real-time PCR (qRT-PCR) analysis showed that transcript levels of CRU1, CRU2, and CRU3 genes were significantly higher in the siz1-2 mutant than in the wild type. Yeast two-hybrid analysis revealed direct interaction of AtSIZ1 with CRU1, CRU2, and CRU3. The sumoylation assay revealed that CRU2, and CRU3 proteins were modified with a small ubiquitin-related modifier (SUMO) by the E3 SUMO ligase activity of AtSIZ1. Additionally, high-performance liquid chromatography (HPLC) analysis showed that the amino acid content was slightly higher in siz1-2 mutant seeds than in wild type seeds. Taken together, our data indicate that AtSIZ1 plays an important role in the accumulation and stability of seed storage proteins through its E3 ligase activity.

Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana

This research was undertaken to investigate the global role of the plant inositol phosphorylceramide synthase (IPCS), a non-mammalian enzyme previously shown to be associated with the pathogen response. RNA-Seq analyses demonstrated that over-expression of inositol phosphorylceramide synthase isoforms AtIPCS1, 2 or 3 in Arabidopsis thaliana resulted in the down-regulation of genes involved in plant response to pathogens. In addition, genes associated with the abiotic stress response to salinity, cold and drought were found to be similarly down-regulated. Detailed analyses of transgenic lines over-expressing AtIPCS1-3 at various levels revealed that the degree of down-regulation is specifically correlated with the level of IPCS expression. Singular enrichment analysis of these down-regulated genes showed that AtIPCS1-3 expression affects biological signaling pathways involved in plant response to biotic and abiotic stress. The up-regulation of genes involved in photosynthesis and lipid localization was also observed in the over-expressing lines.

Parental-genome dosage effects on the transcriptome of F1 hybrid triploid embryos of Arabidopsis thaliana

Genomic imprinting in the seed endosperm could be due to unequal parental-genome contribution effects in triploid endosperm tissue that trigger parent-of-origin specific activation and/or silencing of loci prone to genomic imprinting. To determine whether genomic imprinting is triggered by unequal parental-genome contribution effects, we generated a whole-genome transcriptome dataset of F1 hybrid triploid embryos (as mimics of F1 hybrid triploid endosperm). For the vast majority of genes, the parental contributions to their expression levels in the F1 triploid hybrid embryos follow a biallelic and linear expression pattern. While allele-specific expression (ASE) bias was detected, such effects were predominantly parent-of-origin independent. We demonstrate that genomic imprinting is largely absent from F1 triploid embryos, strongly suggesting that neither triploidy nor unequal parental-genome contribution are key triggers of genomic imprinting in plants. However, extensive parental-genome dosage effects on gene expression were observed between the reciprocal F1 hybrid embryos, particularly for genes involved in defence response and nutrient reservoir activity, potentially leading to the seed size differences between reciprocal triploids. We further determined that unequal parental-genome contribution in F1 triploids can lead to overexpression effects that are parent-of-origin dependent, and which are not observed in diploid or tetraploid embryos in which the parental-genome dosage is balanced. Overall, our study demonstrates that neither triploidy nor unequal parental-genome contribution is sufficient to trigger imprinting in plant tissues, suggesting that genomic imprinting is an intrinsic and unique feature of the triploid seed endosperm.

MYC2, MYC3, and MYC4 function redundantly in seed storage protein accumulation in Arabidopsis

Basic helix-loop-helix transcription factors (TFs), namely MYC2, MYC3, and MYC4, interact with Jasmonate Zim-domain proteins and are their direct targets. These TFs have been shown to function synergistically to control Arabidopsis growth and development. Our results showed similar MYC2, MYC3, and MYC4 expression patterns during Arabidopsis seed development, which remained relatively high during seed mid-maturation. MYC2, MYC3, and MYC4 acted redundantly in seed size, weight control, and in regulating seed storage protein accumulation. Triple mutants produced the largest seeds and single and double mutants' seeds were much larger than those of wild type. The weight of triple mutants' seeds was significantly higher than that of wild-type seeds, which was accompanied by an increase in seed storage protein contents. Triple mutants' seeds presented a marked decrease in 2S amounts relative to those in wild-type seeds. Liquid chromatography tandem mass spectra sequencing results indicated that both the relative abundance and the peptide number of CRA1 and CRU3 were greatly increased in triple mutants compared to wild type. The expression of 2S1-2S5 decreased and that of CRA1 and CRU3 increased in triple mutants relative to those in wild types during seed development, which might have contributed to the low 2S and high 12S contents in triple mutants. Our results contribute to understanding the function of MYC2, MYC3, and MYC4 on seed development, and provide promising targets for genetic manipulations of protein-producing crops to improve the quantity and quality of seed storage proteins.

SHORT HYPOCOTYL UNDER BLUE1 or HAIKU2 mixepression alters canola and Arabidopsis seed development

Canola (Brassica napus) is a widely cultivated species and provides important resources of edible vegetable oil, biodiesel production and animal feed. Seed development in Arabidopsis and canola shares a similar path: an early proliferation of endosperm to form a large seed cavity, followed by a second phase in which the embryo grows to replace the endosperm. In Arabidopsis, the seed reaches almost its final volume before the enlargement of the embryo. SHORT HYPOCOTYL UNDER BLUE1 (SHB1) is a key regulatory gene of seed development with a broad expression beyond endosperm development. By contrast, its two target genes, MINISEED3 (MINI3) and HAIKU2 (IKU2), are narrowly expressed in early developing endosperm and early embryo. We overexpressed SHB1 in canola to explore the possibility of altering seed development. As an alternative strategy, we expressed the canola IKU2 ortholog in Arabidopsis endosperm under the control of a stronger MINI3 promoter. SHB1 targeted canola orthologs of Arabidopsis MINI3 and IKU2 and caused a significantly increased seed mass. Overaccumulation of IKU2 in the early stage of Arabidopsis seed development also significantly increased the final seed mass. Our studies provide a strong case for increasing the final seed mass by manipulating endosperm proliferation at a rather early developmental stage in crops.

Seed Embryo Development Is Regulated via an AN3-MINI3 Gene Cascade

In agriculture, seed mass is one of the most important components related to seed yield. MINISEED3 (MINI3) which encodes the transcriptional activator WRKY10, is thought to be a pivotal regulator of seed mass. In Arabidopsis SHORT HYPOCOTYL UNDER BLUE1 (SHB1) associates with the promoter of MINI3, regulating embryo cell proliferation (both cell division and elongation), which, in turn, modulates seed mass. Furthermore, the recruitment of SHB1 via MINI3 to both its cognate promoter and that of IKU2 implies a two-step amplification for countering the low expression level of IKU2, which is thought to function as a molecular switch for seed cavity enlargement. However, it is largely unknown how embryo cell proliferation, which encompasses both cell division and elongation, is regulated by SHB1 and MINI3 function. Here, we show that a loss of function mutation within the transcriptional coactivator ANGUSTIFOLIA3 (AN3), increases seed mass. Further, AN3 associates with the MINI3 promoter in vivo. Genetic evidence indicates that the absence of MINI3 function suppresses the decrease of cell number observed in an3-4 mutants by regulating cell division and in turn inhibits increased cell size of the an3-4 line by controlling cell elongation. Thus, seed embryo development is modulated via an AN3-MINI3 gene cascade. This regulatory model provides a deeper understanding of seed mass regulation, which may in turn lead to increased crop yields.

A role for seed storage proteins in Arabidopsis seed longevity

Proteomics approaches have been a useful tool for determining the biological roles and functions of individual proteins and identifying the molecular mechanisms that govern seed germination, vigour and viability in response to ageing. In this work the dry seed proteome of four Arabidopsis thaliana genotypes, that carry introgression fragments at the position of seed longevity quantitative trait loci and as a result display different levels of seed longevity, was investigated. Seeds at two physiological states, after-ripened seeds that had the full germination ability and aged (stored) seeds of which the germination ability was severely reduced, were compared. Aged dry seed proteomes were markedly different from the after-ripened and reflected the seed longevity level of the four genotypes, despite the fact that dry seeds are metabolically quiescent. Results confirmed the role of antioxidant systems, notably vitamin E, and indicated that protection and maintenance of the translation machinery and energy pathways are essential for seed longevity. Moreover, a new role for seed storage proteins (SSPs) was identified in dry seeds during ageing. Cruciferins (CRUs) are the most abundant SSPs in Arabidopsis and seeds of a triple mutant for three CRU isoforms (crua crub cruc) were more sensitive to artificial ageing and their seed proteins were highly oxidized compared with wild-type seeds. These results confirm that oxidation is involved in seed deterioration and that SSPs buffer the seed from oxidative stress, thus protecting important proteins required for seed germination and seedling formation.

Dynamic proteomics emphasizes the importance of selective mRNA translation and protein turnover during Arabidopsis seed germination

During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [(35)S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment.

Generation of VHH antibodies against the Arabidopsis thaliana seed storage proteins

Antibodies and antibody derived fragments are excellent tools for the detection and purification of proteins. However, only few antibodies targeting Arabidopsis seed proteins are currently available. Here, we evaluate the process to make antibody libraries against crude protein extracts and more particularly to generate a VHH phage library against native Arabidopsis thaliana seed proteins. After immunising a dromedary with a crude Arabidopsis seed extract, we cloned the single-domain antigen-binding fragments from their heavy-chain only antibodies in a phage display vector and selected nanobodies (VHHs) against native Arabidopsis seed proteins. For 16 VHHs, the corresponding antigens were identified by affinity purification and MS/MS analysis. They were shown to bind the major Arabidopsis seed storage proteins albumin and globulin (14 to albumin and 2 to globulin). All 16 VHHs were suitable primary reagents for the detection of the Arabidopsis seed storage proteins by ELISA. Furthermore, several of the anti-albumin VHHs were used successfully for storage protein localisation via electron microscopy. The easy cloning, selection and production, together with the demonstrated functionality and applicability, strongly suggest that the VHH antibody format will play a more prominent role in future protein research, in particular for the study of native proteins.

Camelina seed transcriptome: a tool for meal and oil improvement and translational research

Camelina (Camelina sativa), a Brassicaceae oilseed, has received recent interest as a biofuel crop and production platform for industrial oils. Limiting wider production of camelina for these uses is the need to improve the quality and content of the seed protein-rich meal and oil, which is enriched in oxidatively unstable polyunsaturated fatty acids that are deleterious for biodiesel. To identify candidate genes for meal and oil quality improvement, a transcriptome reference was built from 2047 Sanger ESTs and more than 2 million 454-derived sequence reads, representing genes expressed in developing camelina seeds. The transcriptome of approximately 60K transcripts from 22 597 putative genes includes camelina homologues of nearly all known seed-expressed genes, suggesting a high level of completeness and usefulness of the reference. These sequences included candidates for 12S (cruciferins) and 2S (napins) seed storage proteins (SSPs) and nearly all known lipid genes, which have been compiled into an accessible database. To demonstrate the utility of the transcriptome for seed quality modification, seed-specific RNAi lines deficient in napins were generated by targeting 2S SSP genes, and high oleic acid oil lines were obtained by targeting FATTY ACID DESATURASE 2 (FAD2) and FATTY ACID ELONGASE 1 (FAE1). The high sequence identity between Arabidopsis thaliana and camelina genes was also exploited to engineer high oleic lines by RNAi with Arabidopsis FAD2 and FAE1 sequences. It is expected that these transcriptomic data will be useful for breeding and engineering of additional camelina seed traits and for translating findings from the model Arabidopsis to an oilseed crop.

Characterization of a cruciferin deficient mutant of Arabidopsis and its utility for overexpression of foreign proteins in plants

Plant seeds naturally accumulate storage reserves (proteins, carbohydrates, lipids) that are mobilized during germination to provide energy and raw materials to support early seedling growth. Seeds have been exploited as bioreactors for the production to foreign materials, but stable, high level expression has been elusive, in part due to the intrinsic bias for producing the natural reserves in their typical proportions. To identify mutants governing seed filling, we screened a population of mutagenized Arabidopsis plants for a mutant that failed to fill its seeds. Here we report the identification of ssp1, a recessive, viable mutant that accumulates approximately 15% less protein than wildtype seeds. Molecular analyses revealed that ssp1 is due to the introduction of a premature stop codon in CRU3, one of the major cruciferin genes. Unlike many other reserve mutants or transgenic lines in which seed storage protein levels are reduced by antisense/RNAi technologies, ssp1 exhibits low level compensation by other reserves, and represents a mutant background that might prove useful for high level expression of foreign proteins. To test this hypothesis, we used a bean phytohemagglutinin (PHA) gene as a reporter and compared PHA expression levels in single copy insertion lines in ssp1 vs. wildtype. These near isogenic lines allow reporter protein levels to be compared without the confounding and sometimes unknown influences of transgene copy number and position effects on gene expression. The ssp1 lines consistently accumulated more PHA than the backcrossed counterparts, with increases ranging from 12% to 126%. This proof of principle study suggests that similar strategies in crop plants may improve the yield of foreign proteins of agronomic and economic interest.

Characterization of Arabidopsis thaliana lines with altered seed storage protein profiles using synchrotron-powered FT-IR spectromicroscopy

Arabidopsis thaliana lines expressing only one cruciferin subunit type (double-knockout; CRUAbc, CRUaBc, or CRUabC) or devoid of cruciferin (triple-knockout; CRU-) or napin (napin-RNAi) were generated using combined T-DNA insertions or RNA interference approaches. Seeds of double-knockout lines accumulated homohexameric cruciferin and contained similar protein levels as the wild type (WT). Chemical imaging of WT and double-knockout seeds using synchrotron FT-IR spectromicroscopy (amide I band, 1650 cm(-1), νC═O) showed that proteins were concentrated in the cell center and protein storage vacuoles. Protein secondary structure features of the homohexameric cruciferin lines showed predominant β-sheet content. The napin-RNAi line had lower α-helix content than the WT. Lines entirely devoid of cruciferin had high α-helix and low β-sheet levels, indicating that structurally different proteins compensate for the loss of cruciferin. Lines producing homohexameric CRUC showed minimal changes in protein secondary structure after pepsin treatment, indicating low enzyme accessibility. The Synchrotron FT-IR technique provides information on protein secondary structure and changes to the structure within the cell.

MicroRNA-mediated repression of the seed maturation program during vegetative development in Arabidopsis

The seed maturation program only occurs during late embryogenesis, and repression of the program is pivotal for seedling development. However, the mechanism through which this repression is achieved in vegetative tissues is poorly understood. Here we report a microRNA (miRNA)–mediated repression mechanism operating in leaves. To understand the repression of the embryonic program in seedlings, we have conducted a genetic screen using a seed maturation gene reporter transgenic line in Arabidopsis (Arabidopsis thaliana) for the isolation of mutants that ectopically express seed maturation genes in leaves. One of the mutants identified from the screen is a weak allele of ARGONAUTE1 (AGO1) that encodes an effector protein for small RNAs. We first show that it is the defect in the accumulation of miRNAs rather than other small RNAs that causes the ectopic seed gene expression in ago1. We then demonstrate that overexpression of miR166 suppresses the derepression of the seed gene reporter in ago1 and that, conversely, the specific loss of miR166 causes ectopic expression of seed maturation genes. Further, we show that ectopic expression of miR166 targets, type III homeodomain-leucine zipper (HD-ZIPIII) genes PHABULOSA (PHB) and PHAVOLUTA (PHV), is sufficient to activate seed maturation genes in vegetative tissues. Lastly, we show that PHB binds the promoter of LEAFY COTYLEDON2 (LEC2), which encodes a master regulator of seed maturation. Therefore, this study establishes a core module composed of a miRNA, its target genes (PHB and PHV), and the direct target of PHB (LEC2) as an underlying mechanism that keeps the seed maturation program off during vegetative development.

Seed development can be conceptually divided into two phases: namely the morphogenesis phase, in which cell division is active and all the major organs are formed, and the maturation phase, in which cells enlarge and storage reserves are synthesized and accumulated. Expression of the seed maturation program is tightly controlled such that it only occurs during the late phase of seed development. To uncover the molecular mechanisms underlying the repression of seed genes during vegetative development, we performed a reporter-assisted genetic screen, and one mutant identified is a weak allele of ARGONAUTE1 (AGO1) that displays ectopic seed gene expression. We then performed a series of transgenic and genetic analyses to search for the molecular mechanisms underlying the mutant phenotype. We first demonstrate that the decrease in miR166 in ago1 is a major cause of the mutant phenotype. Further, we show that the targets of miR166, type III HD-ZIP transcription factors PHB and PHV, are sufficient for derepressing seed maturation genes in seedlings, likely by binding directly to the promoter of a master regulator gene of maturation. Thus, this work establishes a miRNA–mediated pathway that represses the embryonic program and also establishes PHB/PHV as direct activators of the maturation program.

Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules

Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome.

Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

BACKGROUND

Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants.

RESULTS

Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots.

CONCLUSION

Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

Activation of a mitochondrial ATPase gene induces abnormal seed development in Arabidopsis

The ATPases associated with various cellular activities (AAA) proteins are widespread in living organisms. Some of the AAA-type ATPases possess metalloprotease activities. Other members constitute the 26S proteasome complexes. In recent years, a few AAA members have been implicated in vesicle-mediated secretion, membrane fusion, cellular organelle biogenesis, and hypersensitive responses (HR) in plants. However, the physiological roles and biochemical activities of plant AAA proteins have not yet been defined at the molecular level, and regulatory mechanisms underlying their functions are largely unknown. In this study, we showed that overexpression of an Arabidopsis gene encoding a mitochondrial AAA protein, ATPase-in-Seed-Development (ASD), induces morphological and anatomical defects in seed maturation. The ASD gene is expressed at a high level during the seed maturation process and in mature seeds but is repressed rapidly in germinating seeds. Transgenic plants overexpressing the ASD gene are morphologically normal. However, seed formation is severely disrupted in the transgenic plants. The ASD gene is induced by abiotic stresses, such as low temperatures and high salinity, in an abscisic acid (ABA)-dependent manner. The ASD protein possesses ATPase activity and is localized into the mitochondria. Our observations suggest that ASD may play a role in seed maturation by influencing mitochondrial function under abiotic stress.

Altered xylem-phloem transfer of amino acids affects metabolism and leads to increased seed yield and oil content in Arabidopsis

Seed development and nitrogen (N) storage depend on delivery of amino acids to seed sinks. For efficient translocation to seeds, amino acids are loaded into the phloem in source leaves and along the long distance transport pathway through xylem-phloem transfer. We demonstrate that Arabidopsis thaliana AMINO ACID PERMEASE2 (AAP2) localizes to the phloem throughout the plant. AAP2 T-DNA insertion lines showed changes in source-sink translocation of amino acids and a decrease in the amount of seed total N and storage proteins, supporting AAP2 function in phloem loading and amino acid distribution to the embryo. Interestingly, in aap2 seeds, total carbon (C) levels were unchanged, while fatty acid levels were elevated. Moreover, branch and silique numbers per plant and seed yield were strongly increased. This suggests changes in N and C delivery to sinks and subsequent modulations of sink development and seed metabolism. This is supported by tracer experiments, expression studies of genes of N/C transport and metabolism in source and sink, and by phenotypic and metabolite analyses of aap2 plants. Thus, AAP2 is key for xylem to phloem transfer and sink N and C supply; moreover, modifications of N allocation can positively affect C assimilation and source-sink transport and benefit sink development and oil yield.

SHORT HYPOCOTYL UNDER BLUE1 associates with MINISEED3 and HAIKU2 promoters in vivo to regulate Arabidopsis seed development

Seed development in Arabidopsis thaliana undergoes an initial phase of endosperm proliferation followed by a second phase in which the embryo grows at the expense of the endosperm. As mature seed size is largely attained during the initial phase, seed size is coordinately determined by the growth of the maternal ovule, endosperm, and embryo. Here, we identify SHORT HYPOCOTYL UNDER BLUE1 (SHB1) as a positive regulator of Arabidopsis seed development that affects both cell size and cell number. shb1-D, a gain-of-function overexpression allele, increases seed size, and shb1, a loss-of-function allele, reduces seed size. SHB1 is transmitted zygotically. The increase in shb1-D seed size is associated with endosperm cellurization, chalazal endosperm enlargement, and embryo development. SHB1 is required for the proper expression of two other genes that affect endosperm development, MINISEED3 (MINI3) and HAIKU2 (IKU2), a WRKY transcription factor gene and a leucine-rich repeat receptor kinase gene. SHB1 associates with both MINI3 and IKU2 promoters in vivo. SHB1 may act with other proteins that bind to MINI3 and IKU2 promoters to promote a large seed cavity and endosperm growth in the early phase of seed development. In the second phase, SHB1 enhances embryo cell proliferation and expansion through a yet unknown IKU2-independent pathway.

An Arabidopsis mutant able to green after extended dark periods shows decreased transcripts of seed protein genes and altered sensitivity to abscisic acid

An Arabidopsis mutant showing an altered ability to green on illumination after extended periods of darkness has been isolated in a screen for genomes uncoupled (gun) mutants. Following illumination for 24 h, 10-day-old dark-grown mutant seedlings accumulated five times more chlorophyll than wild-type seedlings and this was correlated with differences in plastid morphology observed by transmission electron microscopy. The mutant has been named greening after extended darkness 1 (ged1). Microarray analysis showed much lower amounts of transcripts of genes encoding seed storage proteins, oleosins, and late embryogenesis abundant (LEA) proteins in 7-day-old seedlings of ged1 compared with the wild type. RNA gel-blot analyses confirmed very low levels of transcripts of seed protein genes in ged1 seedlings grown for 2-10 d in the dark, and showed higher amounts of transcripts of photosynthesis-related genes in illuminated 10-day-old dark-grown ged1 seedlings compared with the wild type. Consensus elements similar to abscisic acid (ABA) response elements (ABREs) were detected in the upstream regions of all genes highly affected in ged1. Germination of ged1 seeds was hypersensitive to ABA, although no differences in ABA content were detected in 7-day-old seedlings. This suggests the mutant may have an altered responsiveness to ABA, affecting expression of ABA-responsive genes and plastid development during extended darkness.

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.

Storage reserve accumulation in Arabidopsis: metabolic and developmental control of seed filling

In the life cycle of higher plants, seed development is a key process connecting two distinct sporophytic generations. Seed development can be divided into embryo morphogenesis and seed maturation. An essential metabolic function of maturing seeds is the deposition of storage compounds that are mobilised to fuel post-germinative seedling growth. Given the importance of seeds for food and animal feed and considering the tremendous interest in using seed storage products as sustainable industrial feedstocks to replace diminishing fossil reserves, understanding the metabolic and developmental control of seed filling constitutes a major focus of plant research. Arabidopsis thaliana is an oilseed species closely related to the agronomically important Brassica oilseed crops. The main storage compounds accumulated in seeds of A. thaliana consist of oil stored as triacylglycerols (TAGs) and seed storage proteins (SSPs). Extensive tools developed for the molecular dissection of A. thaliana development and metabolism together with analytical and cytological procedures adapted for very small seeds have led to a good description of the biochemical pathways producing storage compounds. In recent years, studies using these tools have shed new light on the intricate regulatory network controlling the seed maturation process. This network involves sugar and hormone signalling together with a set of developmentally regulated transcription factors. Although much remains to be elucidated, the framework of the regulatory system controlling seed filling is coming into focus.

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

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

Analysis of the Arabidopsis histidine kinase ATHK1 reveals a connection between vegetative osmotic stress sensing and seed maturation

To cope with water stress, plants must be able to effectively sense, respond to, and adapt to changes in water availability. The Arabidopsis thaliana plasma membrane His kinase ATHK1 has been suggested to act as an osmosensor that detects water stress and initiates downstream responses. Here, we provide direct genetic evidence that ATHK1 not only is involved in the water stress response during early vegetative stages of plant growth but also plays a unique role in the regulation of desiccation processes during seed formation. To more comprehensively identify genes involved in the downstream pathways affected by the ATHK1-mediated response to water stress, we created a large-scale summary of expression data, termed the AtMegaCluster. In the AtMegaCluster, hierarchical clustering techniques were used to compare whole-genome expression levels in athk1 mutants with the expression levels reported in publicly available data sets of Arabidopsis tissues grown under a wide variety of conditions. These experiments revealed that ATHK1 is cotranscriptionally regulated with several Arabidopsis response regulators, together with two proteins containing novel sequences. Since overexpression of ATHK1 results in increased water stress tolerance, our observations suggest a new top-down route to increasing drought resistance via receptor-mediated increases in sensing water status, rather than through genetically engineered changes in downstream transcription factors or specific osmolytes.

Systematic studies of 12S seed storage protein accumulation and degradation patterns during Arabidopsis seed maturation and early seedling germination stages

Seed storage proteins (SSPs) are important for seed germination and early seedling growth. We studied the accumulation and degradation profiles of four major Arabidopsis 12S SSPs using a 2-DE scheme combined with mass spectrometric methods. On the 2-DE map of 23 dpa (days post anthesis) siliques, 48 protein spots were identified as putative full-length or partial alpha, beta subunits. Only 9 of them were found in 12 dpa siliques with none in younger than 8 dpa siliques, indicating that the accumulation of 12S SSPs started after the completion of cell elongation processes both in siliques and in developing seeds. The length and strength of transcription activity for each gene determined the final contents of respective SSP. At the beginning of imbibition, 68 SSP spots were identified while only 2 spots were found at the end of the 4 d germination period, with alpha subunits degraded more rapidly than the beta subunits. The CRC alpha subunit was found to degrade from its C-terminus with conserved sequence motifs. Our data provide an important basis for understanding the nutritional value of developing plant seeds and may serve as a useful platform for other species.

Phosphorylation of the 12 S globulin cruciferin in wild-type and abi1-1 mutant Arabidopsis thaliana (thale cress) seeds

Cruciferin (a 12 S globulin) is the most abundant storage protein in the seeds of Arabidopsis thaliana (thale cress) and other crucifers, sharing structural similarity with the cupin superfamily of proteins. Cruciferin is synthesized as a precursor in the rough endoplasmic reticulum. Subunit assembly is accompanied by structural rearrangements involving proteolysis and disulfide-bond formation prior to deposition in protein storage vacuoles. The A. thaliana cv. Columbia genome contains four cruciferin loci, two of which, on the basis of cDNA analysis, give rise to three alternatively spliced variants. Using MS, we confirmed the presence of four variants encoded by genes At4g28520.1, At5g44120.3, At1g03880.1 and At1g3890.1 in A. thaliana seeds. Two-dimensional gel electrophoresis, along with immunological detection using anti-cruciferin antiserum and antibodies against phosphorylated amino acid residues, revealed that cruciferin was the major phosphorylated protein in Arabidopsis seeds and that polymorphism far exceeded that predicted on the basis of known isoforms. The latter may be attributed, at least in part, to phosphorylation site heterogeneity. A total of 20 phosphorylation sites, comprising nine serine, eight threonine and three tyrosine residues, were identified by MS. Most of these are located on the IE (interchain disulfide-containing) face of the globulin trimer, which is involved in hexamer formation. The implications of these findings for cruciferin processing, assembly and mobilization are discussed. In addition, the protein phosphatase 2C-impaired mutant, abi1-1, was found to exhibit increased levels of cruciferin phosphorylation, suggesting either that cruciferin may be an in vivo target for this enzyme or that abi1-1 regulates the protein kinase/phosphatase system required for cruciferin phosphorylation.

Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings

During development of plant seeds, embryos import nutrients and store massive amounts of reserves. Seed reserves are rapidly degraded and mobilized to support seedling development after germination. HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE 2 (HSI2) of Arabidopsis thaliana is a B3 DNA-binding domain protein that represses the transcription of sugar-inducible reporter gene. Although disruption of HSI2 or HSI2-Like 1 (HSL1) did not affect growth, seeds with disruption of both HSI2 and HSL1 (KK mutant) developed abortive seedlings that stopped growing 7-9 days after imbibition. KK seedlings developed swollen hypocotyls that accumulated seed storage proteins and oil on medium containing sucrose or other metabolizable sugars, and calluses developed from KK seedlings also accumulated seed storage reserves. The expression of seed maturation genes, which include LEAFY COTYLEDON-type master regulators, in KK seedlings depended on the concentration of sucrose, suggesting that sugar controls the expression of seed maturation genes. Our results suggest that HSI2 and HSL1 repress the sugar-inducible expression of the seed maturation program in seedlings and play an essential role in regulating the transition from seed maturation to seedling growth.

Gene expression during seed maturation in Brassica napus in relation to the induction of secondary dormancy

Gene expression in two cultivars of Brassica napus (AC Excel and DH12075) has been compared at the full-size embryo, desiccation, and mature stages of seed development. Seed of these cultivars differ in their potential to exhibit secondary dormancy following environmental stress; Excel has high potential and DH12075 has low potential. A majority of genes were down-regulated during maturation in both cultivars but a significant number of differences in gene expression between the cultivars were apparent in the transition from full-size embryo to mature seed. However, most differences were apparent in the desiccation stage and some of the differences were in genes related to signaling processes and protein biosynthesis. We suggest that the propensity of Brassica seeds to manifest secondary dormancy may be determined by changes in gene expression that occur during late seed development.

The turnip mutant of Arabidopsis reveals that LEAFY COTYLEDON1 expression mediates the effects of auxin and sugars to promote embryonic cell identity

The transition from embryonic to vegetative growth marks an important developmental stage in the plant life cycle. The turnip (tnp) mutant was identified in a screen for modifiers of POLARIS expression, a gene required for normal root growth. Mapping and molecular characterization of tnp shows that it represents a gain-of-function mutant of LEAFY COTYLEDON1 (LEC1), due to a promoter mutation. This results in the ectopic expression of LEC1, but not of other LEC genes, in vegetative tissues. The LEC class of genes are known regulators of embryogenesis, involved in the control of embryonic cell identity by currently unknown mechanisms. Activation of the LEC-dependent pathway in tnp leads to the loss of hypocotyl epidermal cell marker expression and loss of SCARECROW expression in the endodermis, the ectopic accumulation of starch and lipids, and the up-regulation of early and late embryonic genes. tnp also shows partial deetiolation during dark growth. Penetrance of the mutant phenotype is strongly enhanced in the presence of exogenous auxin and sugars, but not by gibberellin or abscisic acid, and is antagonized by cytokinin. We propose that the role of LEC1 in embryonic cell fate control requires auxin and sucrose to promote cell division and embryonic differentiation.

Characterization of a novel putative zinc finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development

Phytohormones play crucial roles in regulating many aspects of plant development. Although much has been learned about the effects of individual hormones, cross-talk between and integration of different hormonal signals are still not well understood. We present a study of MINI ZINC FINGER 1 (MIF1), a putative zinc finger protein from Arabidopsis, and suggest that it may be involved in integrating signals from multiple hormones. MIF1 homologs are highly conserved among seed plants, each characterized by a very short sequence containing a central putative zinc finger domain. Constitutive overexpression of MIF1 caused dramatic developmental defects, including dwarfism, reduced apical dominance, extreme longevity, dark-green leaves, altered flower morphology, poor fertility, reduced hypocotyl length, spoon-like cotyledons, reduced root growth, and ectopic root hairs on hypocotyls and cotyledons. In addition, 35S::MIF1 seedlings underwent constitutive photomorphogenesis in the dark, with root growth similar to that in the light. Furthermore, 35S::MIF1 seedlings were demonstrated to be non-responsive to gibberellin (GA) for cell elongation, hypersensitive to the GA synthesis inhibitor paclobutrazol (PAC) and abscisic acid (ABA), and hyposensitive to auxin, brassinosteroid and cytokinin, but normally responsive to ethylene. The de-etiolation defect could not be rescued by the hormones tested. Consistent with these observations, genome-scale expression profiling revealed that 35S::MIF1 seedlings exhibited decreased expression of genes involved in GA, auxin and brassinosteroid signaling as well as cell elongation/expansion, and increased expression of ABA-responsive genes. We propose that MIF1, or the protein(s) with which MIF1 interacts, is involved in mediating the control of plant development by multiple hormones.

Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts

An EST database has been generated for coffee based on sequences from approximately 47,000 cDNA clones derived from five different stages/tissues, with a special focus on developing seeds. When computationally assembled, these sequences correspond to 13,175 unigenes, which were analyzed with respect to functional annotation, expression profile and evolution. Compared with Arabidopsis, the coffee unigenes encode a higher proportion of proteins related to protein modification/turnover and metabolism-an observation that may explain the high diversity of metabolites found in coffee and related species. Several gene families were found to be either expanded or unique to coffee when compared with Arabidopsis. A high proportion of these families encode proteins assigned to functions related to disease resistance. Such families may have expanded and evolved rapidly under the intense pathogen pressure experienced by a tropical, perennial species like coffee. Finally, the coffee gene repertoire was compared with that of Arabidopsis and Solanaceous species (e.g. tomato). Unlike Arabidopsis, tomato has a nearly perfect gene-for-gene match with coffee. These results are consistent with the facts that coffee and tomato have a similar genome size, chromosome karyotype (tomato, n=12; coffee n=11) and chromosome architecture. Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information.

Two naturally occurring deletion mutants of 12S seed storage proteins in Arabidopsis thaliana

Two naturally occurring Arabidopsis mutants, Cape Verde Islands and Monte (Mr-0), with aberrant 12S seed storage protein (SSP) profiles have been identified by SDS-PAGE. In both mutants, one of the 12S globulin bands is missing while a new band of lower molecular mass is present. Tandem mass spectrometry-mass spectrometry (MS/MS) analyses of the mutant peptides have revealed that both are shorter variants of 12S globulin with deletion sites detected within the alpha-subunits of 12S globulin cruciferin B (CRB) and C (CRC), respectively. Sequence analyses of the genomic DNA flanking the deletion sites have demonstrated that both deletions occurred at the genomic level. These two mutants are referred to as CRBDelta12 and CRCDelta13 with the delta sign indicating a deletion and the number indicating amino acids deleted. Alignment of these two mutant sequences with that of soybean A3B4 subunit, for which the crystal structure was determined recently, have revealed that the CRCDelta13 deletion is located in a hypervariable/disordered region, and will probably not affect the structure of the hexameric globulin. The CRBDelta12 deletion, however, is located in a binding region that is thought to be important for the hexamer formation. However, CRBDelta12 appears to accumulate normally as judged by its band intensity relative to the other SSP subunits on the protein gels. Thus it seems that the seed can, to a certain extent, tolerate some mutations in its storage proteins.

Patterns of protein oxidation in Arabidopsis seeds and during germination

Increased cellular levels of reactive oxygen species are known to occur during seed development and germination, but the consequences in terms of protein degradation are poorly characterized. In this work, protein carbonylation, which is an irreversible oxidation process leading to a loss of function of the modified proteins, has been analyzed by a proteomic approach during the first stages of Arabidopsis (Arabidopsis thaliana) seed germination. In the dry mature seeds, the legumin-type globulins (12S cruciferins) were the major targets. However, the acidic alpha-cruciferin subunits were carbonylated to a much higher extent than the basic (beta) ones, consistent with a model in which the beta-subunits are buried within the cruciferin molecules and the alpha-subunits are more exposed to the outside. During imbibition, various carbonylated proteins accumulated. This oxidation damage was not evenly distributed among seed proteins and targeted specific proteins as glycolytic enzymes, mitochondrial ATP synthase, chloroplastic ribulose bisphosphate carboxylase large chain, aldose reductase, methionine synthase, translation factors, and several molecular chaperones. Although accumulation of carbonylated proteins is usually considered in the context of aging in a variety of model systems, this was clearly not the case for the Arabidopsis seeds since they germinated at a high rate and yielded vigorous plantlets. The results indicate that the observed specific changes in protein carbonylation patterns are probably required for counteracting and/or utilizing the production of reactive oxygen species caused by recovery of metabolic activity in the germinating seeds.

LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3

Arabidopsis ABSCISIC ACID INSENSEITIVE3 (ABI3), FUSCA3 (FUS3) and LEAFY COTYLEDON1 (LEC1) encode key transcription factors that control seed maturation events, including seed storage protein (SSP) accumulation. Although lec1 mutations are known to down-regulate SSP gene expression as the fus3 or abi3 mutation does, the mechanisms by which LEC1 regulates SSP gene expression are largely unknown compared with the mechanisms utilized by FUS3 or ABI3. We expressed LEC1 ectopically in transgenic plants using an artificial dexamethasone (Dex) induction system. The ectopic expression of LEC1 also resulted in the induction of FUS3 and ABI3 expression, which preceded the induction of SSP expression. The expression of FUS3 and ABI3 was found to be down-regulated in developing siliques of the lec1 mutant. Furthermore, the levels of ectopic SSP induction by LEC1 were greatly or moderately reduced in transgenic plants with an abi3 or fus3 mutant background, respectively. LEC1-induced ectopic expression of the At1g62290 aspartic protease gene, which was identified to be regulated preferentially by FUS3, was more severely affected in the fus3 mutant than in the abi3 mutant. From these data, we suggest that LEC1 controls the expression of the SSP genes in a hierarchical manner, which involves ABI3 and FUS3.

Control of seed mass and seed yield by the floral homeotic gene APETALA2

APETALA2 (AP2) is best known for its role in the regulation of flower meristem and flower organ identity and development in Arabidopsis. We show here that AP2 also plays an important role in determining seed size, seed weight, and the accumulation of seed oil and protein. We demonstrate genetically that AP2 acts through the maternal sporophyte and endosperm genomes to control seed weight and seed yield. Thus, AP2 functions outside the boundaries of flower meristem and flower organ development to affect agronomically relevant traits in Arabidopsis.

Isolation of the gene encoding Carrot leafy cotyledon1 and expression analysis during somatic and zygotic embryogenesis

The Arabidopsis thaliana LEC1 gene regulates embryo morphology and seed maturation. For a better understanding of its function, we isolated a carrot (Daucus carota L. cv. US-Harumakigosun) counterpart of this gene, C-LEC1, from a cDNA library of carrot somatic embryos, since carrot is a better model plant for preparing large quantities of somatic embryos at the same developmental stage. The predicted amino acid sequence of C-LEC1 is similar to that of LEC1 and contains regions that are conserved in the heme-activated protein 3 (HAP3) subunit of plants, animals and microorganisms. C-LEC1 expression was detected in embryogenic cells, somatic embryos, and developing seeds. In situ hybridization analysis revealed C-LEC1 expression in the peripheral region of the embryos but not in the endosperm. Expression of C-LEC1 driven by Arabidopsis LEC1 promoter was able to complement the defects of the Arabidopsis lec1-1 mutant. These results suggest that C-LEC1 is a functional homolog of Arabidopsis LEC1, an important regulator of zygotic and somatic embryo development.

Regulation of storage protein gene expression in Arabidopsis

The expression of seed storage proteins is under tight developmental regulation and represents a powerful model system to study the regulation of gene expression during plant development. In this study, we show that three homologous B3 type transcription factors regulate the model storage protein gene, At2S3, via two distinct mechanisms: FUSCA3 (FUS3) and LEAFY COTYLEDON2 (LEC2) activate the At2S3 promoter in yeast suggesting that they regulate At2S3 by directly binding its promoter; ABSCISIC ACID INSENSITIVE3 (ABI3), however, appears to act more indirectly on At2S3, possibly as a cofactor in an activation complex. In accordance with this, FUS3 and LEC2 were found to act in a partially redundant manner and differently from ABI3 in planta: At2S3 expression is reduced to variable and sometimes only moderate extent in fus3 and lec2 single mutants but is completely abolished in the lec2 fus3 double mutant. In addition, we found that FUS3 and LEC2 expression patterns, together with an unsuspected regulation of FUS3 by LEC2, enable us to explain the intriguing expression pattern of At2S3 in lec2 or fus3 single mutants. Based on these results, we present a model of At2S3 regulation and discuss its implications for other aspects of seed maturation.

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

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

Storage protein accumulation in the absence of the vacuolar processing enzyme family of cysteine proteases

The role(s) of specific proteases in seed protein processing is only vaguely understood; indeed, the overall role of processing in stable protein deposition has been the subject of more speculation than direct investigation. Seed-type members of the vacuolar processing enzyme (VPE) family were hypothesized to perform a unique function in seed protein processing, but we demonstrated previously that Asn-specific protein processing in developing Arabidopsis seeds occurs independently of this VPE activity. Here, we describe the unexpected expression of vegetative-type VPEs in developing seeds and test the role(s) of all VPEs in seed storage protein accumulation by systematically stacking knockout mutant alleles of all four members (alphaVPE, betaVPE, gammaVPE, and deltaVPE) of the VPE gene family in Arabidopsis. The complete removal of VPE function in the alphavpe betavpe gammavpe deltavpe quadruple mutant resulted in a total shift of storage protein accumulation from wild-type processed polypeptides to a finite number of prominent alternatively processed polypeptides cleaved at sites other than the conserved Asn residues targeted by VPE. Although alternatively proteolyzed legumin-type globulin polypeptides largely accumulated as intrasubunit disulfide-linked polypeptides with apparent molecular masses similar to those of VPE-processed legumin polypeptides, they showed markedly altered solubility and protein assembly characteristics. Instead of forming 11S hexamers, alternatively processed legumin polypeptides were deposited primarily as 9S complexes. However, despite the impact on seed protein processing, plants devoid of all known functional VPE genes appeared unchanged with regard to protein content in mature seeds, relative mobilization rates of protein reserves during germination, and vegetative growth. These findings indicate that VPE-mediated Asn-specific proteolytic processing, and the physiochemical property changes attributed to this specific processing step, are not required for the successful deposition and mobilization of seed storage protein in the protein storage vacuoles of Arabidopsis seeds.

Vacuolar processing enzymes are essential for proper processing of seed storage proteins in Arabidopsis thaliana

The proprotein precursors of storage proteins are post-translationally processed to produce their respective mature forms within the protein storage vacuoles of maturing seeds. To investigate the processing mechanism in vivo, we isolated Arabidopsis mutants that accumulate detectable amounts of the precursors of the storage proteins, 12 S globulins and 2 S albumins, in their seeds. All six mutants isolated have a defect in the beta VPE gene. VPE (vacuolar processing enzyme) is a cysteine proteinase with substrate specificity toward an asparagine residue. We further generated various mutants lacking different VPE isoforms: alpha VPE, beta VPE, and/or gamma VPE. More than 90% of VPE activity is abolished in the beta vpe-3 seeds, and no VPE activity is detected in the alpha vpe-1/beta vpe-3/gamma vpe-1 seeds. The triple mutant seeds accumulate no properly processed mature storage proteins. Instead, large amounts of storage protein precursors are found in the seeds of this mutant. In contrast to beta vpe-3 seeds, which accumulate both precursors and mature storage proteins, the other single (alpha vpe-1 and gamma vpe-1) and double (alpha vpe-1/gamma vpe-1) mutants accumulate no precursors in their seeds at all. Therefore, the vegetative VPEs, alpha VPE and gamma VPE, are not necessary for precursor processing in the presence of beta VPE, but partly compensates for the deficiency in beta VPE in beta vpe-3 seeds. In the absence of functional VPEs, a proportion of pro2S albumin molecules are alternatively cleaved by aspartic proteinase. This cleavage by aspartic proteinase is promoted by the initial processing of pro2S albumins by VPE. Our overall results suggest that seed-type beta VPE is most essential for the processing of storage proteins, and that the vegetative-type VPEs and aspartic proteinase complement beta VPE activity in this processing.

Protein interaction analysis of SCF ubiquitin E3 ligase subunits from Arabidopsis

Ubiquitin E3 ligases are a diverse family of protein complexes that mediate the ubiquitination and subsequent proteolytic turnover of proteins in a highly specific manner. Among the several classes of ubiquitin E3 ligases, the Skp1-Cullin-F-box (SCF) class is generally comprised of three 'core' subunits: Skp1 and Cullin, plus at least one F-box protein (FBP) subunit that imparts specificity for the ubiquitination of selected target proteins. Recent genetic and biochemical evidence in Arabidopsis thaliana suggests that post-translational turnover of proteins mediated by SCF complexes is important for the regulation of diverse developmental and environmental response pathways. In this report, we extend upon a previous annotation of the Arabidopsis Skp1-like (ASK) and FBP gene families to include the Cullin family of proteins. Analysis of the protein interaction profiles involving the products of all three gene families suggests a functional distinction between ASK proteins in that selected members of the protein family interact generally while others interact more specifically with members of the F-box protein family. Analysis of the interaction of Cullins with FBPs indicates that CUL1 and CUL2, but not CUL3A, persist as components of selected SCF complexes, suggesting some degree of functional specialization for these proteins. Yeast two-hybrid analyses also revealed binary protein interactions between selected members of the FBP family in Arabidopsis. These and related results are discussed in terms of their implications for subunit composition, stoichiometry and functional diversity of SCF complexes in Arabidopsis.

A high-throughput system for two-hybrid screening based on growth curve analysis in microtiter plates

The yeast two-hybrid system is a powerful tool for identifying novel protein-protein interactions. In general, biochemical marker genes such as lacZ are exploited for indirect quantification of the interaction, and commonly involve the conduct of rather laborious beta-galactosidase assays. This paper describes a simple alternative method based on growth curve analysis of yeast cultures that is amenable to microtiter plate format, and therefore allows the quantification of large numbers of yeast two-hybrid combinations. The analyzed results of yeast cultures grown in microtiter plates were compared with those obtained from the classical beta-galactosidase assay. We conclude that the method presented here is reproducible, of equal or greater sensitivity than the beta-galactosidase assay, and can be further adapted for application to the conduct of large-scale, automated yeast two-hybrid experiments.

Storage proteins

Plants accumulate storage substances such as starch, lipids and proteins in certain phases of development. Storage proteins accumulate in both vegetative and reproductive tissues and serve as a reservoir to be used in later stages of plant development. The accumulation of storage protein is thus beneficial for the survival of plants. Storage proteins are also an important source of dietary plant proteins. Here, we summarize the genome organization and regulation of gene expression of storage protein genes in Arabidopsis.

The three typical aspartic proteinase genes of Arabidopsis thaliana are differentially expressed

Genomic sequencing has identified three different typical plant aspartic proteinases in the genome of Arabidopsis thaliana, named Pasp-A1, A2 and A3. A1 is identical to a cDNA we had previously isolated and the two others produce proteins 81 and 63% identical to that predicted protein. Sequencing of the aspartic proteinase protein purified from Arabidopsis seeds showed that the peptides are derived from two of these genes, A1 and A2. Using gene specific probes, we have analyzed RNA from different tissues and found these three genes are differentially expressed. A1 mRNA is detected in all tissues analyzed and more abundant in leaves during the light phase of growth. The other two genes are expressed either primarily in flowers (A3) or in seeds (A2). Insitu hybridization demonstrated that all three genes are expressed in many cells of the seeds and developing seed pods. The A1 and A3 genes are expressed in the sepals and petals of flowers as well as the outer layer of the style, but are not expressed in the transmitting tract or on the stigmatal surface. The A2 gene is weakly expressed only in the transmitting tissue of the style. All three genes are also expressed in the guard cells of sepals. These data suggest multiple roles for aspartic proteinases besides those proposed in seeds.