A major cysteine proteinase, EPB, in germinating barley seeds: structure of two intronless genes and regulation of expression

How Cysteine Protease Gene PtCP5 Affects Seed Germination by Mobilizing Storage Proteins in Populus trichocarpa

In higher plants, seed storage proteins are deposited in protein storage vacuoles (PSVs) and degraded by protease, especially cysteine proteases, as a source of nitrogen for seed germination. In this study, a cathepsin B-like cysteine protease PtCP5, which is important for seed germination and pollen development, was first cloned in Populus trichocarpa. The GUS staining of the ProPtCP5-GUS reporter line showed that PtCP5 is expressed in the roots, stems, leaves, flowers, siliques and seeds of Arabidopsis. We reveal that PtCP5 is present in plasma membrane and co-localizes with the plasma membrane marker REM1.3. Both seed germination and early seedling development are slower in OX-PtCP5 transgenic Arabidopsis when compared with the wild-type. Further analysis revealed that, when stained with toluidine blue, the observed storage protein accumulation was lower in OX-PtCP5 than in the wild-type. Our results also show that the number of abnormal pollen grains is higher and the germination rate of pollen is lower in OX-PtCP5 than in the wild-type. These results indicate that PtCP5 is an important factor in mobilizing storage proteins and that the proper expression of PtCP5 is necessary for both pollen and seed maturation and germination. This study sheds further light on the biological functions of cysteine proteases and provides further reference for seed development research on woody plants.

Tissue-Specific Proteome and Subcellular Microscopic Analyses Reveal the Effect of High Salt Concentration on Actin Cytoskeleton and Vacuolization in Aleurone Cells during Early Germination of Barley

Cereal grain germination provides the basis for crop production and requires a tissue-specific interplay between the embryo and endosperm during heterotrophic germination involving signalling, protein secretion, and nutrient uptake until autotrophic growth is possible. High salt concentrations in soil are one of the most severe constraints limiting the germination of crop plants, affecting the metabolism and redox status within the tissues of germinating seed. However, little is known about the effect of salt on seed storage protein mobilization, the endomembrane system, and protein trafficking within and between these tissues. Here, we used mass spectrometry analyses to investigate the protein dynamics of the embryo and endosperm of barley (Hordeum vulgare, L.) at five different early points during germination (0, 12, 24, 48, and 72 h after imbibition) in germinated grains subjected to salt stress. The expression of proteins in the embryo as well as in the endosperm was temporally regulated. Seed storage proteins (SSPs), peptidases, and starch-digesting enzymes were affected by salt. Additionally, microscopic analyses revealed an altered assembly of actin bundles and morphology of protein storage vacuoles (PSVs) in the aleurone layer. Our results suggest that besides the salt-induced protein expression, intracellular trafficking and actin cytoskeleton assembly are responsible for germination delay under salt stress conditions.

Genome-wide transcriptional response of papain-like cysteine protease-mediated resistance against Xanthomonas oryzae pv. oryzae in rice

Transgenic rice overexpressing PLCP attenuated the virulence of Xanthomonas oryzae pv. oryzae through extensive activation of transduction signal and transcription activities that orchestrate downstream responses including the biosynthesis of secondary metabolites and up-regulation of several pathogenesis-related proteins. High-throughput transcriptome investigations of plant immunity highlight the complexity of gene networks leading to incompatible interaction with the pathogen. Accumulating findings implicate papain-like cysteine proteases (PLCPs) as a central hub in plant defense. While diverse roles of PLCPs in different pathosystems have become more evident, information on gene networks and signaling pathways necessary to orchestrate downstream responses are lacking. To understand the biological significance of cysteine protease against Xanthomonas oryzae pv. oryzae, PLCP overexpression and knockout rice lines were generated. The pathogenicity test revealed the attenuation of Xanthomonas oryzae pv. oryzae race K3a virulence in transgenic lines which is ascribed to high hydrogen peroxide and free salicylic acid accumulation. Next-generation sequencing of RNA from transgenic and wild-type plants identified 1597 combined differentially expressed genes, 1269 of which were exclusively regulated in the transgenic libraries. It was found that PLCP aids rice to circumvent infection through the extensive activation of transduction signal and transcription factors that orchestrate downstream responses, including up-regulation of multiple pathogenesis-related proteins and biosynthesis of secondary metabolites.

Insights on the Proteases Involved in Barley and Wheat Grain Germination

Seed storage proteins must be hydrolyzed by proteases to deliver the amino acids essential for embryo growth and development. Several groups of proteases involved in this process have been identified in both the monocot and the dicot species. This review focuses on the implication of proteases during germination in two cereal species, barley and wheat, where proteolytic control during the germination process has considerable economic importance. Formerly, the participation of proteases during grain germination was inferred from reports of proteolytic activities, the expression of individual genes, or the presence of individual proteins and showed a prominent role for papain-like and legumain-like cysteine proteases and for serine carboxypeptidases. Nowadays, the development of new technologies and the release of the genomic sequences of wheat and barley have permitted the application of genome-scale approaches, such as those used in functional genomics and proteomics. Using these approaches, the repertoire of proteases known to be involved in germination has increased and includes members of distinct protease families. The development of novel techniques based on shotgun proteomics, activity-based protein profiling, and comparative and structural genomics will help to achieve a general view of the proteolytic process during germination.

A tiered approach to genome-wide association analysis for the adherence of hulls to the caryopsis of barley seeds reveals footprints of selection

BACKGROUND

Seeds of domesticated barley are grouped into two distinct types, which differ in morphology. Caryopses covered by adaxial (palea) and abaxial (lemma) hulls that tightly adhere to the pericarp at maturity give rise to hulled seeds whereas caryopses without adhering hulls give rise to naked seeds. The naked caryopsis character is an essential trait regarding the end use of barley.

RESULTS

To uncover the genetic basis of the trait, a genome-wide association study (GWAS) has been performed in a panel comprising 222 2-rowed and 303 6-rowed spring barley landrace accessions. In addition to the well-described Nud locus on chromosome 7H, three novel loci showed strong associations with the trait: the first locus on 2H was specifically detected in 6-rowed accessions, the second locus on 3H was found in 2-rowed accessions from Eurasia and the third locus on 6H was revealed in 6-rowed accessions from Ethiopia. PCR analysis of naked accessions also confirmed the absence of a 17 kb region harboring the Nud gene on chromosome 7H for all but one naked accession. The latter was characterized by a slightly variant phenotype of the caryopsis.

CONCLUSION

Our findings provide evidence of the pervasiveness of the 17 kb deletion in spring barley from different geographic regions and at the same time reveal genomic footprints of selection in naked barley, which follow both geographic and morphological patterns.

Plant Proteases: From Key Enzymes in Germination to Allies for Fighting Human Gluten-Related Disorders

Plant proteases play a crucial role in many different biological processes along the plant life cycle. One of the most determinant stages in which proteases are key protagonists is the plant germination through the hydrolysis and mobilization of other proteins accumulated in seeds and cereal grains. The most represented proteases in charge of this are the cysteine proteases group, including the C1A family known as papain-like and the C13 family also called legumains. In cereal species such as wheat, oat or rye, gluten is a very complex mixture of grain storage proteins, which may affect the health of sensitive consumers like celiac patients. Since gluten proteins are suitable targets for plant proteases, the knowledge of the proteases involved in storage protein mobilization could be employed to manipulate the amount of gluten in the grain. Some proteases have been previously found to exhibit promising properties for their application in the degradation of known toxic peptides from gluten. To explore the variability in gluten-degrading capacities, we have now analyzed the degradation of gluten from different wheat cultivars using several cysteine proteases from barley. The wide variability showed highlights the possibility to select the protease with the highest potential to alter grain composition reducing the gluten content. Consequently, new avenues could be explored combining genetic manipulation of proteolytic processes with silencing techniques to be used as biotechnological tools against gluten-related disorders.

Role of Papain-Like Cysteine Proteases in Plant Development

Papain-like cysteine proteases (PLCP) are prominent peptidases found in most living organisms. In plants, PLCPs was divided into nine subgroups based on functional and structural characterization. They are key enzymes in protein proteolysis and involved in numerous physiological processes. In this paper, we reviewed the updated achievements of physiological roles of plant PLCPs in germination, development, senescence, immunity, and stress responses.

The roles of cysteine proteases and phytocystatins in development and germination of cereal seeds

Proteolysis is an important process for development and germination of cereal seeds. Among the many types of proteases identified in plants are the cysteine proteases (CPs) of the papain and legumain families, which play a crucial role in hydrolysing storage proteins during seed germination as well as in processing the precursors of these proteins and the inactive forms of other proteases. Moreover, all of the tissues of cereal seeds undergo progressive degradation via programed cell death, which is integral to their growth. In view of the important roles played by proteases, their uncontrolled activity could be harmful to the development of seeds and young seedlings. Thus, the activities of these enzymes are regulated by intracellular inhibitors called phytocystatins (PhyCys). The phytocystatins inhibit the activity of proteases of the papain family, and the presence of an additional motif in their C-termini allows them to also regulate the activity of members of the legumain family. A balance between the levels of cysteine proteases and phytocystatins is necessary for proper cereal seed development, and this is maintained through the antagonistic activities of gibberellins (GAs) and abscisic acid (ABA), which regulate the expression of the corresponding genes. Transcriptional regulation of cysteine proteases and phytocystatins is determined by cis-acting elements located in the promoters of these genes and by the expression of their corresponding transcription factors (TFs) and the interactions between different TFs.

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas

BACKGROUND

Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi.

RESULTS

We sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated.

CONCLUSION

The present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031.

Rice bifunctional phytocystatin is a dual modulator of legumain and papain-like proteases

Phytocystatins are well-known inhibitors of C1A cysteine proteinases. However, previous research has revealed legumain (C13) protease inhibition via a carboxy-extended phytocystatin. Among the 12 phytocystatins genes in rice, OcXII is the only gene possessing this carboxy-terminal extension. The specific legumain inhibition activity was confirmed, in our work, using a recombinant OcXII harboring only the carboxy-terminal domain and this part did not exhibit any effect on papain-like activities. Meanwhile, rice plants silenced at the whole OcXII gene presented higher legumain and papain-like proteolytic activities, resulting in a faster initial seedling growth. However, when germinated under stressful alkaline conditions, OcXII-silenced plants exhibited impaired root formation and delayed shoot growth. Interestingly, the activity of OcXII promoter gene was detected in the rice seed scutellum region, and decreases with seedling growth. Seeds from these plants also exhibited slower growth at germination under ABA or alkaline conditions, while maintaining very high levels of OcXII transcriptional activation. This likely reinforces the proteolytic control necessary for seed germination and growth. In addition, increased legumain activity was detected in OcXII RNAi plants subjected to a fungal elicitor. Overall, the results of this study highlight the association of OcXII with not only plant development processes, but also with stress response pathways. The results of this study reinforce the bifunctional ability of carboxy-extended phytocystatins in regulating legumain proteases via its carboxy-extended domain and papain-like proteases by its amino-terminal domain.

Production of barley endoprotease B2 in Pichia pastoris and its proteolytic activity against native and recombinant hordeins

Barley (Hordeum vulgare L.) cysteine proteases are of fundamental biological importance during germination but may also have a large potential as commercial enzyme. Barley cysteine endoprotease B2 (HvEPB2) was expressed in Pichia pastoris from a pPICZαA based construct encoding a HvEPB2 C-terminal truncated version (HvEPB2ΔC) and a proteolytic resistant His6 tag. Maximum yield was obtained after 4 days of induction. Recombinant HvEPB2ΔC (r-HvEPB2ΔC) was purified using a single step of Ni(2+)-affinity chromatography. Purified protein was evaluated by SDS-PAGE, Western blotting and activity assays. A purification yield of 4.26 mg r-HvEPB2ΔC per L supernatant was obtained. r-HvEPB2ΔC follows first order kinetics (Km=12.37 μM) for the substrate Z-Phe-Arg-pNA and the activity was significantly inhibited by the cysteine protease specific inhibitors E64 and leupeptin. The temperature optimum for r-HvEPB2ΔC was 60°C, thermal stability T50 value was 44°C and the pH optimum was 4.5. r-HvEPB2ΔC was incubated with native purified barley seed storage proteins for up to 48 h. After 12h, r-HvEPB2ΔC efficiently reduced the C and D hordeins almost completely, as evaluated by SDS-PAGE. The intensities of the B and γ hordein bands decreased continuously over the 48 h. No degradation occurred in the presence of E64. Recombinant hordeins (B1, B3 and γ1) were expressed in Escherichia coli. After 2h of incubation with r-HvEPB2ΔC, an almost complete degradation of γ1 and partial digests of hordein B1 and B3 were observed.

Expression profile of maize (Zea mays) scutellar epithelium during imbibition

The scutellum is a shield-shaped structure surrounding the embryo axis in grass species. The scutellar epithelium (Sep) is a monolayer of cells in contact with the endosperm. The Sep plays an important role during seed germination in the secretion of gibberellins and hydrolytic enzymes and in the transport of the hydrolized products to the growing embryo. We identified 30 genes predominantly expressed after imbibition in the Sep as compared to other parts of the scutellum. A high proportion of these genes is involved in metabolic processes. Some other identified genes are involved in the synthesis or modification of cell walls, which may be reflected in the changes of cell shape and cell wall composition that can be observed during imbibition. One of the genes encodes a proteinase that belongs to a proteinase family typical of carnivorous plants. Almost nothing is known about their role in other plants or organs, but the scutellar presence may point to a "digestive" function during germination. Genes involved in the production of energy and the transport of peptides were also identified.

A cathepsin F-like peptidase involved in barley grain protein mobilization, HvPap-1, is modulated by its own propeptide and by cystatins

Among the C1A cysteine proteases, the plant cathepsin F-like group has been poorly studied. This paper describes the molecular and functional characterization of the HvPap-1 cathepsin F-like protein from barley. This peptidase is N-glycosylated and has to be processed to become active by its own propeptide being an important modulator of the peptidase activity. The expression pattern of its mRNA and protein suggest that it is involved in different proteolytic processes in the barley plant. HvPap-1 peptidase has been purified in Escherichia coli and the recombinant protein is able to degrade different substrates, including barley grain proteins (hordeins, albumins, and globulins) stored in the barley endosperm. It has been localized in protein bodies and vesicles of the embryo and it is induced in aleurones by gibberellin treatment. These three features support the implication of HvPap-1 in storage protein mobilization during grain germination. In addition, a complex regulation exerted by the barley cystatins, which are cysteine protease inhibitors, and by its own propeptide, is also described.

Oral enzyme therapy for celiac sprue

Celiac sprue is an inflammatory disease of the small intestine caused by dietary gluten and treated by adherence to a life-long gluten-free diet. The recent identification of immunodominant gluten peptides, the discovery of their cogent properties, and the elucidation of the mechanisms by which they engender immunopathology in genetically susceptible individuals have advanced our understanding of the molecular pathogenesis of this complex disease, enabling the rational design of new therapeutic strategies. The most clinically advanced of these is oral enzyme therapy, in which enzymes capable of proteolyzing gluten (i.e., glutenases) are delivered to the alimentary tract of a celiac sprue patient to detoxify ingested gluten in situ. In this chapter, we discuss the key challenges for discovery and preclinical development of oral enzyme therapies for celiac sprue. Methods for lead identification, assay development, gram-scale production and formulation, and lead optimization for next-generation proteases are described and critically assessed.

Molecular Cloning and Expression Analysis of Triticale Phytocystatins During Development and Germination of Seeds

Three triticale cDNAs encoding inhibitors of cysteine endopeptidases, belonging to phytocystatins, have been identified and designated as TrcC-1, TrcC-4 and TrcC-5. Full-length cDNAs of TrcC-1 (617 bp) and TrcC-4 (940 bp), as well as a fragment of TrcC-5 cDNA (369 bp), were obtained. A high-level identity of the deduced amino acid sequence of TrcCs with other known phytocystatins, especially with wheat and barley, has been observed. Moreover, the presence of conserved domain, containing the G and W residues, the sequence of QxVxG and the sequence of LARFAV, characteristic for plant cysteine endopeptidase inhibitors, has been noted. The profiles of TrcC-1 and TrcC-5 mRNA levels in the developing seeds of two triticale cultivars that differ in their resistance to preharvest sprouting (Zorro and Disco) were similar. However, the expression of TrcC-4 was, higher in the developing seeds, and in the scutellum of germinating seeds of a cultivar more resistant to preharvest sprouting (Zorro) than in the less resistant (Disco). Additionally, the expression of TrcC-4 remained longer in developing seeds of Zorro as compared to Disco. The performed studies suggest that TrcC-4 might have an influence on the higher resistance of Zorro cultivar to preharvest sprouting.

Wheat cysteine proteases triticain alpha, beta and gamma exhibit mutually distinct responses to gibberellin in germinating seeds

We cloned three novel papain-type cysteine proteases (CPs), triticain alpha, beta and gamma, from 1-d-germinating wheat seeds. Triticain alpha, beta and gamma were constituted with 461, 472 and 365 amino acid residues, respectively, and had Cys-His-Asn catalytic triads as well as signal and propeptide sequences. Triticain gamma contained a putative vacuole-sorting sequence. Phylogenetic analysis showed that these CPs were divided into mutually different clusters. Triticain alpha and gamma mRNAs were expressed in seeds at an early stage of maturation and at the stage of germination 2d after imbibition, while triticain beta mRNA appeared shortly after imbibition. The expression of mRNAs for triticain alpha and gamma was suppressed by uniconazol, a gibberellin synthesis inhibitor. All the three CP mRNAs were strongly expressed in both embryo and aleurone layers. These results suggest that triticain alpha, beta and gamma play differential roles in seed maturation as well as in digestion of storage proteins during germination.

Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools

Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley (Hordeum vulgare) grain maturation, desiccation, and germination in two tissue fractions (starchy endosperm/aleurone and embryo/scutellum) using the Affymetrix Barley1 GeneChip. To aid data evaluation, Arabidopsis thaliana MapMan and PageMan tools were adapted to barley. The analyses allow a number of conclusions: (1) Cluster analysis revealed a smooth transition in transcription programs between late seed maturation and germination within embryo tissues, but not in the endosperm/aleurone. (2) More than 12,000 transcripts are stored in the embryo of dry barley grains, many of which are presumably activated during germination. (3) Transcriptional activation of storage reserve mobilization events occurs at an early stage of germination, well before radicle protrusion. (4) Key genes of gibberellin (GA) biosynthesis are already active during grain maturation at a time when abscisic acid peaks suggesting the formation of an endogenous store of GA in the aleurone. This GA probably acts later during germination in addition to newly synthesized GA. (5) Beside the well-known role of GA in gene activation during germination spatiotemporal expression data and cis-element searches in homologous rice promoters confirm an equally important gene-activating role of abscisic acid during this developmental period. The respective regulatory webs are linked to auxin and ethylene controlled networks. In summary, new bioinformatics PageMan and MapMan tools developed in barley have been successfully used to investigate in detail the transcriptome relationships between seed maturation and germination in an important crop plant.

Induced expression of oryzain alpha gene encoding a cysteine proteinase under stress conditions

Oryzain alpha-A, a cysteine proteinase gene was cloned from rice (Oryza sativa L. cv. Aichi-asahi) leaves infected with Magnaporthe grisea. The protein sequence deduced for oryzain alpha-A shares high identity with that of oryzain alpha, a gene expressed in germinating rice seed. Oryzain alpha-A gene expression was induced by the blast fungus, Magnaporthe grisea, and the transcript level was even higher in the compatible interaction with rice than in the incompatible interaction. Expression of oryzain alpha-A was also inducible by wounding, ultraviolet radiation, and treatment with salicylic acid and abscisic acid, with no expression induced by methyl jasmonate. The function of oryzain alpha-A in cell death in rice is discussed.

Gliadain, a gibberellin-inducible cysteine proteinase occurring in germinating seeds of wheat, Triticum aestivum L., specifically digests gliadin and is regulated by intrinsic cystatins

We cloned a new cysteine proteinase of wheat seed origin, which hydrolyzed the storage protein gliadin almost specifically, and was named gliadain. Gliadain mRNA was expressed 1 day after the start of seed imbibition, and showed a gradual increase thereafter. Gliadain expression was suppressed when uniconazol, a gibberellin synthesis inhibitor, was added to germinating seeds. Histochemical detection with anti-gliadain serum indicated that gliadain was present in the aleurone layer and also that its expression intensity increased in sites nearer the embryo. The enzymological characteristics of gliadain were investigated using recombinant glutathione S-transferase (GST)-progliadain fusion protein produced in Escherichia coli. The GST-progliadain almost specifically digested gliadin into low molecular mass peptides. These results indicate that gliadain is produced via gibberellin-mediated gene activation in aleurone cells and secreted into the endosperm to digest its storage proteins. Enzymologically, the GST-progliadain hydrolyzed benzyloxycarbonyl-Phe-Arg-7-amino-4-methylcoumarin (Z-Phe-Arg-NH(2)-Mec) at K(m) = 9.5 microm, which is equivalent to the K(m) value for hydrolysis of this substrate by cathepsin L. Hydrolysis was inhibited by two wheat cystatins, WC1 and WC4, with IC(50) values of 1.7 x 10(-8) and 5.0 x 10(-8) m, respectively. These values are comparable with those found for GST-progliadain inhibition by E-64 and egg-white cystatin, and are consistent with the possibility that, in germinating wheat seeds, gliadain is under the control of intrinsic cystatins.

Heterologous Expression, Purification, Refolding, and Structural-Functional Characterization of EP-B2, a Self-Activating Barley Cysteine Endoprotease

We describe the heterologous expression in Escherichia coli of the proenzyme precursor to EP-B2, a cysteine endoprotease from germinating barley seeds. High yields (50 mg/l) of recombinant proEP-B2 were obtained from E. coli inclusion bodies in shake flask cultures following purification and refolding. The zymogen was rapidly autoactivated to its mature form under acidic conditions at a rate independent of proEP-B2 concentration, suggesting a cis mechanism of autoactivation. Mature EP-B2 was stable and active over a wide pH range and efficiently hydrolyzed a recombinant wheat gluten protein, alpha2-gliadin, at sequences with known immunotoxicity in celiac sprue patients. The X-ray crystal structure of mature EP-B2 bound to leupeptin was solved to 2.2 A resolution and provided atomic insights into the observed subsite specificity of the endoprotease. Our findings suggest that orally administered proEP-B2 may be especially well suited for treatment of celiac sprue.

Complete, precise, and innocuous loss of multiple introns in the currently intronless, active cathepsin L-like genes, and inference from this event

Retrotransposition typically generates pseudogenes. Here we demonstrate a different fate of the retro-processed genes through a novel mechanism in which the retro-processed genes still maintain their sequence intactness and the original functions. We show that the shrimp cathepsin L (CatL) gene MeCatL has lost all of its five introns. Also, ProEPB, the ancestor of the CatL-like barley EPBs and rice REP1, has lost all of its three introns. The multiple introns in a gene might have been eliminated simultaneously and precisely at the original locus for the CatL-like genes of shrimp, barley, rice, Drosophila, and Theileria. We reason that retrotransposition is not responsible for the generation of a processed active intronless (PAI) gene when the gene product retains its sequence intactness and its original function. We propose that double-strand-break repair (DSBR) machinery might play a role in cDNA-mediated homologous recombination (cDMHR) that causes the loss of introns. The cDMHR/DSBR pathway is probably a fundamental mechanism for intron loss in PAI genes and in some asymmetric-intron genes.

Structural, biological, and evolutionary relationships of plant food allergens sensitizing via the gastrointestinal tract

The recently completed genome sequence of the model plant species Arabidopsis has been estimated to encode over 25,000 proteins, which, on the basis of their function, can be classified into structural and metabolic (the vast majority of plant proteins), protective proteins, which defend a plant against invasion by pathogens or feeding by pests, and storage proteins, which proved a nutrient store to support germination in seeds. It is now clear that almost all plant food allergens are either protective or storage proteins. It is also becoming evident that those proteins that trigger the development of an allergic response through the gastrointestinal tract belong primarily to two large protein superfamilies: (1) The cereal prolamin superfamily, comprising three major groups of plant food allergens, the 2S albumins, lipid transfer proteins, and cereal alpha-amylase/trypsin inhibitors, which have related structures, and are stable to thermal processing and proteolysis. They include major allergens from Brazil nut, peanuts, fruits, such as peaches, and cereals, such as rice and wheat; (2) The cupin superfamily, comprising the major globulin storage proteins from a number of plant species. The globulins have been found to be allergens in plant foods, such as peanuts, soya bean, and walnut; (3) The cyteine protease C1 family, comprising the papain-like proteases from microbes, plants, and animals. This family contains two notable allergens that sensitize via the GI tract, namely actinidin from kiwi fruit and the soybean allergen, Gly m Bd 30k/P34. This study describes the properties, structures, and evolutionary relationships of these protein families, the allergens that belong to them, and discusses them in relation to the role protein structure may play in determining protein allergenicity.

Shrimp cathepsin L encoded by an intronless gene has predominant expression in hepatopancreas, and occurs in the nucleus of oocyte

We have cloned the cDNA and genomic DNA of an active intronless cathepsin L from Metapenaeus ensis. The encoded enzyme has the shortest prosequence among cathepsin L subgroup. It was predominantly expressed in hepatopancreas with an expression level of at least 10 times higher than in any other tissues. It also has expression in stomach, intestine, eye, testis, ovary and muscle. Western blots visualized the mature enzyme in hepatopancreas and a procathepsin L in ovary, intestine and stomach. Metapenaeus cathepsin L (MeCatL) is localized in the large digestive vacuole of the digestive B cell of hepatopancreas. MeCatL has a role in food digestion. An interesting finding is that it exists in the nucleus of oocyte. MeCatL might have a specified physiological role in the nucleus of oocyte. MeCatL might also have a house-keeping function as is suggested for mammalian cathepsin L.

A cathepsin B-like cysteine protease gene from Hordeum vulgare (gene CatB) induced by GA in aleurone cells is under circadian control in leaves

A barley cDNA clone encoding a putative cysteine protease with sequence homology to cathepsin B from mammalian cells has been characterized. This barley gene (CatB) is ubiquitously expressed, its mRNA being detected in leaves and roots, immature, mature and germinating embryos, in developing endosperms, and in aleurones upon germination, as assessed by northern blot analysis. The CatB mRNA expression in leaves increased by cold shock (6 degrees C), was not affected by wounding, and was under circadian control. These transcripts increased in the aleurone upon germination, whereas those for a cystatin encoding gene (Icy), that inhibits commercial cathepsin B in vitro, decreased. Gibberellin (GA) treatment of isolated barley aleurones induced and abscisic acid (ABA) repressed the steady-state levels of CatB mRNA, while Icy expression had an opposite pattern of mRNA accumulation in aleurones treated with GA. No response to GA or ABA was detected in leaves.

SAD: a new DOF protein from barley that activates transcription of a cathepsin B-like thiol protease gene in the aleurone of germinating seeds

Functional analysis of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, has identified a GA-responsive complex (GARC) as a tripartite element containing a pyrimidine-box motif 5'-CCTTTT-3'. We describe here the characterization of a new barley gene (Sad gene) encoding a transcription factor (SAD) of the DNA binding with One Finger (DOF) class that binds to the pyrimidine box in vitro and activates transcription of a GA-induced protease promoter in bombarded aleurone layers. RT-PCR and in situ hybridization analyses showed that the Sad transcripts accumulated in all tissues analysed, being especially abundant in the scutellum and aleurone cells upon seed germination. The SAD protein, expressed in bacteria, binds in a specific manner to two oligonucleotides containing the sequence 5'-G/CCTTTT/C-3', derived from the promoter region of the Al21 gene encoding a cathepsin B-like cysteine protease. Although the Sad transcript accumulation did not respond to external GA-incubation in aleurone cells, in transient expression experiments in co-bombarded aleurone layers, SAD trans-activated transcription from the Al21 promoter in a similar manner as did GAMYB, a MYB protein previously shown to respond to GA and to activate several hydrolase gene promoters in barley aleurone cells. In vivo interaction between the GAMYB and SAD proteins was shown in the yeast two-hybrid system, where GAMYB potentiates the SAD trans-activation capacity through interaction with its C-terminal domain.

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.

Maturation of barley cysteine endopeptidase expressed in Trichoderma reesei is distorted by incomplete processing

Maturation of barley cysteine endopeptidase B (EPB) in Trichoderma reesei was studied with metabolic in hibitors, Western blotting, and immuno microscopy. The inactive 42-kDa recombinant EPB proprotein, first detected in apical cells, was sequentially processed in a time-dependent manner to a secreted polypeptide of 38.5 kDa, and thereafter, to polypeptides of 37.5, 35.5, and 32 kDa exhibiting enzyme activity both in the hyphae and culture medium. The sizes of the different forms of recombinant EPB were in accordance with molecular masses calculated from the deduced amino acid sequence, assuming cleavage at four putative Kex2p sites present in the 42-kDa proprotein. Both the liquid and the zymogram in-gel activity assays indicated that the 32-kDa enzyme produced in T. reesei in vivo was 2 kDa larger and four times less active than the endogenous EPB. Brefeldin A treatment prevented the last Kex2p processing step of EPB from a 35.5- to a 32-kDa protein. This coincided with a significant increase in the immuno-gold label for EPB and in modified Golgi-like bodies, which suggests that the processing step probably took place in medial Golgi. A 30.5-kDa EPB polypeptide was observed when glycosylation was inhibited by tunicamycin (TM) or when deglycosylation was carried out enzymatically. Deglycosylation increased the enzyme activity twofold, which was also indicated by an increased fluorescence by TM treatment in the zymogram in-gel activity assay. Simultaneous incubation with TM and monensin produced a peptide of 31.5 kDa. Therefore, monensin may inhibit the final processing step of an unglycosylated EPB by an unknown protease in the fungus. In any case, the final recombinant EPB product in Trichoderma differs from the mature endogenous 30-kDa enzyme produced in barley.

Purification of a cysteine proteinase from Carica candamarcensis L. and cloning of a genomic putative fragment coding for this enzyme

We describe the purification of a cysteine proteinase from latex of Carica candamarcensis, hereby designated CC23. The enzyme has been purified by ion-exchange chromatography and behaves electrophoretically as a monomer of M(r) 23,000 and optimal pH of 8.0. It displays a basic isoelectric point, has one cysteine residue in the active site by titration with E-64, confirmed by DNA sequencing, and responds to proteinase inhibitors as a classic cysteine proteinase. The K(m) and k(cat)/K(m) for CC23 using BAPNA were respectively 14.7 +/- 1.8 x 10(-4) M and 1.3 x 10(3) M(-1) s(-1). Therefore, the catalytic efficiency of CC23 is sixfold higher than that of CC-I, another proteinase from the same plant. DNA primers were designed to amplify by PCR a genomic sequence related to this enzyme. An 895-bp DNA fragment was cloned and sequenced. It shows strong homology with chymopapain isoform IV from C. papaya. The translated sequence is similar to that of chymopapain isoform II (73%) and CC-III (77%) from C. candamarcensis.

Multiple mode regulation of a cysteine proteinase gene expression in rice

In many plants, cysteine proteinases play essential roles in a variety of developmental and physiological processes. In rice (Oryza sativa), REP-1 is a primary cysteine proteinase responsible for the digestion of seed storage proteins to provide nutrients to support the growth of young seedlings. In the present study, the gene encoding REP-1 was isolated, characterized, and designated as OsEP3A. An OsEP3A-specific DNA probe was used to study the effect of various factors on the expression of OsEP3A in germinating seeds and vegetative tissues of rice. The expression of OsEP3A is hormonally regulated in germinating seeds, spatially and temporally regulated in vegetative tissues, and nitrogen-regulated in suspension-cultured cells. The OsEP3A promoter was linked to the coding sequence of the reporter gene, gusA, which encodes beta-glucuronidase (GUS), and the chimeric gene was introduced into the rice genome. The OsEP3A promoter is sufficient to confer nitrogen regulation of GUS expression in suspension-cultured cells. Histochemical studies also indicate that the OsEP3A promoter is sufficient to confer the hormonal regulation of GUS expression in germinating seeds. These studies demonstrate that in rice the REP-1 protease encoded by OsEP3A may play a role in various physiological responses and processes, and that multiple mechanisms regulate the expression of OsEP3A.

Hormonal regulation of a cysteine proteinase gene, EPB-1, in barley aleurone layers: cis- and trans-acting elements involved in the co-ordinated gene expression regulated by gibberellins and abscisic acid

The synthesis of EPB, a cysteine proteinase responsible for the degradation of seed endosperm storage proteins in barley (Hordeum vulgare), is induced by gibberellins (GA) and repressed by abscisic acid (ABA). The EPB gene family consists of two very similar members, EPB-1 and EPB-2, with the former being more highly induced by GA. We have functionally characterized the cis-acting elements in the EPB-1 promoter and determined that a gibberellin response element (GARE), a pyrimidine box and an upstream element are necessary for GA induction. By comparison with the promoters of alpha-amylase genes, which are also induced by GA, we suggest that GARE is coupled with the upstream element and the pyrimidine box to form a GA response complex. In addition, we have shown that the 3'-untranslated/untranscribed region of the EPB-1 gene is required for a low background expression in the absence of GA. Constitutive expression of a transcription factor, GAMyb, in the absence of GA leads to the transactivation of EPB-1 expression in a dosage dependent manner with the highest level comparable to that in fully GA-induced tissue. Co-expression of a truncated version of GAMyb containing only the DNA binding domain blocks the GA-induction of EPB-1, further supporting the role of GAMyb in the regulation of gene expression. Although ABA is very effective in blocking the GA induction of EPB-1, it has no effect on the GAMyb-mediated expression of EPB-1. We suggest that ABA acts upstream of the formation of functional GAMyb which co-ordinates the hormonal regulation of a diverse group of genes in cereal aleurone layers, including those encoding EPB and alpha-amylases.

Cloning and characterization of TPE4A, a thiol-protease gene induced during ovary senescence and seed germination in pea

A cDNA clone encoding a thiol-protease (TPE4A) was isolated from senescent ovaries of pea (Pisum sativum) by reverse transcriptase-polymerase chain reaction. The deduced amino acid sequence of TPE4A has the conserved catalytic amino acids of papain. It is very similar to VSCYSPROA, a thiol-protease induced during seed germination in common vetch. TPE4A mRNA levels increase during the senescence of unpollinated pea ovaries and are totally suppressed by treatment with gibberellic acid. In situ hybridization indicated that TPE4A mRNA distribution in senescent pea ovaries is different from that of previously reported thiol-proteases induced during senescence, suggesting the involvement of different proteases in the mobilization of proteins from senescent pea ovaries. TPE4A is also induced during the germination of pea seeds, indicating that a single protease gene can be induced during two different physiological processes, senescence and germination, both of which require protein mobilization.

An abscisic acid-induced protein kinase, PKABA1, mediates abscisic acid-suppressed gene expression in barley aleurone layers

The phytohormone abscisic acid (ABA) induces genes-encoding proteins involved in desiccation tolerance and dormancy in seeds, but ABA also suppresses gibberellin (GA)-responsive genes encoding hydrolytic enzymes essential for postgermination growth. A unique serine/threonine protein kinase, PKABA1 mRNA, up-regulated by ABA in seeds, has been identified. In this report, the effect of PKABA1 on the signal transduction pathway mediating ABA induction and suppression of genes has been determined in aleurone layers of barley seeds. Two groups of gene constructs were introduced to barley aleurone layers by using particle bombardment: the reporter constructs containing the coding sequence of beta-glucuronidase gene linked to hormone-responsive promoters and the effector constructs containing the coding region of protein kinases linked to a constitutive promoter. Constitutive expression of PKABA1 drastically suppressed expression of low- and high-pI alpha-amylase and protease genes induced by GA. However, the presence of PKABA1 had only a small effect on the ABA induction of a gene encoding a late embryogenesis abundant protein, HVA1. Our results indicate that PKABA1 acts as a key intermediate in the signal transduction pathway leading to the suppression of GA-inducible gene expression in cereal aleurone layers.