Molecular analysis of the effects of the lys 3a gene on the expression of Hor loci in developing endosperms of barley (Hordeum vulgare L.)

Structural and expressional analysis of the B-hordein genes in Tibetan hull-less barley

The B-hordein gene family was analyzed from two Tibetan hull-less barley cultivars Z09 and Z26 (Hordeum vulgare subsp. vulgare). Fourteen B-hordein genes, designated BZ09-2 to BZ09-5 (from Z09) and BZ26-1 to BZ26-10 (from Z26), were sequenced. Seven of them, similar to a previously reported BZ09-1 from Z09, were predicted to encode putative active proteins each with a signal peptide, a repetitive domain, and a C-terminal region; seven of them were predicted to be pseudogenes. The B-hordein gene family was analyzed using all known representatives of B-hordein sequences and two most similar LMW-GSs of Triticum aestivum. Alignment of these seven putative proteins with known B-hordeins and two most similar LMW-GSs of T. aestivum revealed that they shared a common motif. A large variation was observed between numbers of repeat units of predicted B-hordeins of Z26 and Z09. Phylogenetic analysis revealed that all BZ26 clones were clustered in a subgroup, and BZ09-1 formed another subgroup by itself in the putative eight active genes. In addition, six 5'-upstream regulatory sequences of the B-hordein genes were isolated from the two accessions by a single oligonucleotide nested PCR, and several different mutations were identified in the cis-acting element GLM and two distinctive sequences (Z09P-2 and Z26P-3). Phylogenetic analysis of 5'-upstream regulatory regions of the B-hordein genes showed that members from the same accession were clustered together except for two distinct members. Quantitative real time PCR analysis indicated distinct expression levels of B-hordein genes in four developing stages of developing grains in two accessions. These findings suggest B-hordein genes have intrinsic differences between accessions, and this knowledge will be useful for incorporating the B-hordeins protein in barley breeding programs.

Analysis of a rare recombination event within the multigenic Hor 2 locus of barley (Hordeum vulgare L.)

A rare recombinant within the multigenic Hor 2 locus of barley was detected by SD-PAGE of hordein fractions from F2 grain from the cross Bomi × P12/3. Analysis of a homozygous F4 line by 2-D IEF/SDS-PAGE showed that recombination between the class I/II and class III subfamilies of genes had occurred, indicating that they are spatially separate within the Hor 2 locus. RFLP analysis using a B hordein-related cDNA clone confirmed that recombination had occurred, while similar analysis using a genomic clone related to γ-type hordein (encoded by the Hor 5/HrdF locus) indicated the order of the two subfamilies of genes on the short arm of chromosome 5, the class I/II genes being closer to the centromere. The results are consistent with the origin of the B hordein gene family from initial duplication of a single ancestral gene to give two genes which diverged to become the ancestors of the class I/II and class III subfamilies. Subsequent cycles of duplication and divergence have resulted in the present high degree of polymorphism.

Suppression of C-hordein synthesis in barley by antisense constructs results in a more balanced amino acid composition

Barley has for feeding purposes a shortage of essential amino acids, especially lysine, threonine, and methionine, and an excess of proline and glutamine. In the present study, we have introduced into barley an antisense construct against C-hordeins, the storage protein with the lowest nutritional quality. SDS-PAGE and reverse phase HPLC revealed a relative reduction in the amounts of C-hordeins and relative increases in the content of the other storage proteins. The five different lines analyzed had lower amounts of proline, glutamic acid/glutamine, and phenylalanine (up to 12%, 6%, and 9% reductions), while the lysine, threonine, and methionine content was increased with up to 16%, 13% and 11%. It is concluded that antisense mediated suppression of C-hordein synthesis may be a promising approach for improving the nutritional value of barley as a feed crop while at the same time reducing the environmental nitrogen load.

Differential gene expression in the developing barley endosperm

Barley prolamin storage proteins account for 50% of the seed proteins. They are encoded by small multigene families that are only expressed in the developing endosperm. Previous work has shown that the major prolamins in barley are characterized by the presence of two or more unrelated structural domains, one of which contains repeated sequences. The non-repetitive domain is homologous with sequences present in other seed proteins found in the seed of mono- and dicotyledonous plants. Comparison of the 5' flanking region of a B1 hordein storage protein gene of barley with those of other prolamin genes (zeins and α-gliadins) reveals short sequences within 600 base pairs (bp) of the translation initiation codon that are strongly conserved. A short sequence at —300 bp seems to be unique to the prolamin genes and is possibly involved in the control of gene expression in the developing cereal endosperm. Six DNA-binding proteins have been identified that might recognize and interact with the putative regulatory sequences identified in the B1 hordein gene. Protease inhibitors account for a large proportion of the salt-soluble proteins of the barley seed, and contain up to 10% lysine. Cloned cDNAs for chymotrypsin inhibitors 1 and 2 have been isolated and characterized. All contain ochre stop condons in the sequences encoding a putative signal peptide. The two inhibitors are encoded by small multigene families that specify several subfamilies of mRNAs. The accumulation of chymotrypsin inhibitors in normal and mutant endosperms of barley is related to the abundances of their mRNAs.

Molecular biology of the grain storage proteins of the Triticeae

Chemical studies show that there are close relationships between the storage proteins of the Triticeae. We have investigated these relationships by the study of the synthesis of the proteins in vivo and in vitro , and by making libraries of double-stranded complementary DNA (cDNA) derived from poly A + RNA isolated from developing endosperms of barley, wheat and rye. These cDNA clones have been used to probe the organization and regulation of expression of the Hor loci in barley. The results suggest that regulation of synthesis is generally achieved by changes in the amounts of mRNA for the different proteins, both in response to time of development and the relative supply of sulphur and nitrogen, although there may also be differences in the relative amounts of mRNA translated. The sequencing of the cDNA clones has shown the im portance of repeated sequences in the evolution of prolamin genes.

The structural and evolutionary relationships of the prolamin storage proteins of barley, rye and wheat

The major endosperm storage proteins of barley, wheat and rye are soluble in aqueous alcohols, either native or after the reduction of disulphide bonds, and can be defined as prolamins. They can be divided into three groups on the basis of their chemical characteristics, notably their molecular mass and amino acid composition, and the chromosomal location of their structural genes. Two of the groups, the high molecular mass prolamins and the sulphur-poor (ω-gliadin-type) prolamins, show clear homology between the three species. The remaining prolamins are characterized by a high content of cysteine. In wheat this is a complex mixture of at least three groups of components that vary in their aggregation properties and N-terminal amino acid sequences. The precise chemical and genetic relationships of those components to each other and to the more clearly defined groups of sulphur-rich prolamins of rye and barley are still not completely understood.

The promoter of the gene Itr1 from barley confers a different tissue specificity in transgenic tobacco

Tissue-specific expression of the gene coding for trypsin inhibitor BTI-CMe in barley (Itr1) occurs during the first half of endosperm development. In transgenic tobacco, the Itr1 promoter drives expression of the beta-glucuronidase reporter gene not only in developing endosperm but also in embryo, cotyledons and the meristematic intercotyledonary zone of germinating seedlings. A promoter fragment extending 343 bp upstream of the translation initiation ATG codon was sufficient for full transgene expression, whereas, the proximal 83 bp segment of the promoter was inactive. Possible reasons for the differences in expression patterns are discussed.

Opportunities for manipulating the seed protein composition of wheat and barley in order to improve quality

Wheat and barley are the major temperate cereals, being used for food, feed and industrial raw material. However, in all cases the quality may be limited by the amount, composition and properties of the grain storage proteins. We describe how a combination of biochemical and molecular studies has led to an understanding of the molecular basis for breadmaking quality in wheat and feed quality in barley, and also provided genes encoding key proteins that determine quality. The control of expression of these genes has been studied in transgenic tobacco plants and by transient expression in cereal protoplasts, providing the basis for the production of transgenic cereals with improved quality characteristics.

Separation of acidic barley endosperm proteins by two-dimensional electrophoresis

Proteins in barley aleurone and starchy endosperm from developing seeds were separated by two-dimensional (2-D) electrophoresis according to O'Farrell's method. The effect of different extraction methods on the separation was compared. The two best extraction methods were compared by amino acid analysis of extracts and residues. Some tissue-specific proteins in both tissues are described. Different methods for transfer of separated proteins onto membranes were compared. Amino terminal and internal sequences were determined after transfer of separated proteins or their proteolytic products onto membranes. Amino acid sequence data allowed the identification of 12 different proteins, while 6 remain unidentified and 8 appeared to have a blocked amino terminal.

Evolutionary relationship of the members of the sulphur-rich hordein family revealed by common antigenic determinants

Five monoclonal antibodies raised against an enriched C hordein fraction have been characterized in detail and were found to be specific for the members of the sulphur-rich hordein family. Two antibodies specific for B hordein polypeptides were identified, one of which reacted predominantly with CNBr cleavage class III polypeptides. γ1 hordein was recognized by two antibodies, of which one also reacted with γ2 hordein and several members of the CNBr cleavage class II B hordein polypeptides. One antibody recognized γ3 hordein but cross-reacted at higher antibody concentration with almost all of the B and C hordein polypeptides. The specificity of the monoclonal antibodies was confirmed by Western blotting of one- or two-dimensionally separated hordein from the B hordein-deficient mutant hor2ca and its wild-type Carlsberg II and the γ3 hordein-deficient genotype Nevsky. The identification of the γ hordein-specific monoclonal antibodies was further supported by immune precipitation of in-vitro transcribed and translated γ2 hordein, and hor2ca and Carlsberg II mRNA translation products. The monoclonal antibodies were used to screen for mutants in γ hordein synthesis. Two mutants, one deficient in γ 1 hordein synthesis and a second in γ 2 or closely related B hordein polypeptides were identified. A model is proposed for the evolution of the sulphur-rich hordein loci Hor5 and Hor2.

Identification of a novel beta-turn-rich repeat motif in the D hordeins of barley

The amino acid sequence of the C-terminal part of a barley D hordein seed protein was deduced from the nucleotide sequence of a partial cDNA. It showed high homology with the HMW glutenin subunits of wheat, both proteins consisting predominately of repeated sequences. Whereas the wheat repeats are based on tri-, hexa- and nonapeptides that are rich in glycine, proline and glutamine, the D hordein also contains eleven copies of a novel unrelated motif: Thr-Thr-Val-Ser. The repeated sequences in the wheat glutenin subunits have been demonstrated to form an unusual spiral supersecondary structure based on beta-turns. Conformational analysis of the Thr-Thr-Val-Ser motif by secondary structure prediction and by circular dichroism spectroscopy of an 18 residue synthetic peptide demonstrates that it also forms beta-turns. Thus, D hordein may also have a spiral structure like that of HMW glutenin, despite the presence of a different repeat motif. This conservation of protein conformation in D hordein and the wheat glutenin subunits may indicate a structural role, perhaps in packing of the proteins within the protein bodies of the developing grain.

Methylation of B-hordein genes in barley endosperm is inversely correlated with gene activity and affected by the regulatory gene Lys3

The methylation status of B-hordein genes in the developing barley endosperm was analyzed by digestion with methylation-sensitive restriction enzymes. Southern blotting revealed specific demethylation of Hpa II sites in DNA from wild-type endosperm, whereas leaf DNA and lys3a mutant endosperm DNA were highly methylated at these sites. Similar methylation patterns were observed at an Ava I site situated at position -260 in the B-hordein promoter. This differential methylation was confirmed by genomic sequencing with ligation-mediated PCR. The analyzed sequence covers most of the B-hordein promoter and includes 10 CpGs from the promoter and 4 CpGs from the adjacent coding region. These sites were all hypomethylated in wild-type endosperm, whereas--except for three partially methylated sites--full methylation was seen in leaf DNA. The four sites in the coding region were partially methylated in lys3a endosperm DNA, but the promoter sites remained highly methylated. The possible role of methylation in the regulatory function of the Lys3 gene product is discussed.

The prolamin storage proteins of cereal seeds: structure and evolution

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The gene for trypsin inhibitor CMe is regulated in trans by the lys 3a locus in the endosperm of barley (Hordeum vulgare L.)

A cDNA encoding trypsin inhibitor CMe from barley endosperm has been cloned and characterized. The longest open reading frame of the cloned cDNA codes for a typical signal peptide of 24 residues followed by a sequence which is identical to the known amino acid sequence of the inhibitor, except for an Ile/Leu substitution at position 59. Southern blot analysis of wheat-barley addition lines has shown that chromosome 3H of barley carries the gene for CMe. This protein is present at less than 2%-3% of the wild-type amount in the mature endosperm of the mutant Risø 1508 with respect to Bomi barley, from which it has been derived, and the corresponding steady state levels of the CMe mRNA are about 1%. One or two copies of the CMe gene (synonym Itc1) per haploid genome have been estimated both in the wild type and in the mutant, and DNA restriction patterns are identical in both stocks, so neither a change in copy number nor a major rearrangement of the structural gene account for the markedly decreased expression. The mutation at the lys 3a locus in Risø 1508 has been previously mapped in chromosome 7 (synonym 5H). A single dose of the wild-type allele at this locus (Lys 3a) restores the expression of gene CMe (allele CMe-1) in chromosome 3H to normal levels.

Molecular cloning of two isoinhibitor forms of chymotrypsin inhibitor 1 (CI-1) from barley endosperm and their expression in normal and mutant barleys

Full-length cDNA clones for barley chymotrypsin inhibitor 1 (CI-1) have been isolated from an endosperm-specific cDNA library. Hybridization and nucleotide sequence analyses indicate that these cDNAs represent two distinct types of CI-1 mRNA which we have called CI-1A and CI-1B. Both mRNAs encode polypeptides of 83 residues (M r=8790 and 8960) which differ at eleven positions. The full-length cDNA sequences do not predict N-terminal signal peptide extensions indicating that CI-1 is synthesized in the mature form in contrast to the homologous proteinase inhibitors of tomato and potato. Northern hybridization experiments show that the CI-1 genes are under strict developmental and organ-specific control. CI-1 transcripts were first detected in the developing barley endosperm between 12 and 14 days after anthesis but no CI-1-related sequences were detected in the RNA preparations from shoots, leaves or roots. The expression of CI-1 was also studied in the high-lysine barley mutants Hiproly, Risø 56 and Risø 1508. Approximately 15-fold (Hiproly) and 4-fold (Risø 56 and 1508) higher levels of CI-1 mRNA were detected in the mutant endosperms compared to normal barley. These results correlate well with the increased deposition of CI-1 in the high-lysine lines and show that the differential expression is controlled mainly at the level of transcription or stability of the mRNA. Using Southern-blots of barley DNA we estimate that there are three copies of CI-1 per haploid genome in both normal and mutant barley lines.

Primary structure and differential expression of beta-amylase in normal and mutant barleys

The primary structure of barley endosperm beta-amylase, an enzyme which catalyses the liberation of maltose from 1,4-alpha-D-glucans, has been deduced from the nucleotide sequence of a cloned full-length cDNA. The mRNA is 1754 nucleotides long [excluding the poly(A) tail] and codes for a polypeptide of 535 amino acids with a relative molecular mass of 59,663. The deduced amino acid sequence was compared with the sequences of ten peptides obtained from the purified enzyme and unambiguous identification was obtained. The N-terminal region of the deduced sequence was identical to a 12-residue cyanogen-bromide-peptide sequence, indicating that beta-amylase is synthesized as the mature protein. A graphic matrix homology plot shows four glycine-rich repeats, each of 11 residues, preceding the C-terminus. Southern blotting of genomic DNA demonstrates that beta-amylase is encoded by a small gene family, while cDNA sequence analysis indicates the presence of at least two types of mRNA in the endosperm. Dot and northern blot analysis show that Hiproly barley contains greatly increased levels of beta-amylase mRNA compared to the normal cultivar Sundance, whereas Risø mutant 1508 contains only trace amounts. These results correlate well with the deposition of beta-amylase during endosperm development in these lines. Low but similar amounts of beta-amylase mRNAs sequences were detected in leaves and shoots from normal and mutant barleys, demonstrating that the mutant lys3a (1508) and lysl (Hiproly) genes do not affect the expression of beta-amylase in these tissues.

Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize

The B-hordeins are the major group of prolamin storage proteins in barley (Hordeum vulgare L.) and they are encoded by a small multigene family that is expressed specifically in the developing endosperm. We report the complete nucleotide sequence of a clone of one B-hordein gene (pBHR184). The cloned gene contains no introns and belongs to the B1 sub-family of B-hordein genes. Comparison of the 5'-flanking sequences of pBHR184 with those of related S-rich prolamin genes from wheat shows that several short sequences within 600 bp upstream of the translation initiation codon are strongly conserved. A sequence that is conserved at around -300 bp in the S-rich prolamins is also conserved at similar locations in genes encoding the two major classes of maize prolamin (the Z19 and Z21 zeins) and appears to be unique to prolamin genes. We discuss the possible role of this '-300 element' in the control of gene expression in the developing cereal endosperm.

Differential effects of high-lysine mutations on the accumulation of individual members of a group of proteins encoded by a disperse multigene family in the endosperm of barley (Hordeum vulgare L.)

The CM proteins are a group of major salt-soluble endosperm proteins encoded by a disperse multigene family. The effects of high-lysine mutations on the net accumulation in barley endosperm of three members of this group (CMa, CMb, and CMe) have been investigated. Genes CMa, CMb and CMe are located in chromosomes 1, 4, and 3 respectively. Protein CMe has been found to be identical with a previously described trypsin inhibitor. The three proteins have been quantified in the different genetic stocks by HPLC. The different high-lysine mutations have different effects on the expression patterns of the three genes: CMe is markedly decreased and CMa and CMb are increased in mutant Risø 1508, whereas all three proteins are decreased in Risø 527 and increased in Risø 7 with respect to the wild-type Bomi; CMa and CMb are increased and CMe is unaffected in mutant Risø 56 with respect to the wild-type Carlsberg II; and protein CMe is markedly decreased in Hiproly barley as compared with its sister line CI4362. The implications of these results in connection with the evolution of CM proteins and with the characterization of high-lysine mutations are discussed.

Specificity of an antibody to a subunit of high-molecular-weight storage protein from wheat seed and its reaction with other cereal storage proteins (prolamins)

An antiserum to subunit 2 from the high-molecular-weight (HMW) subunits of the glutenin fraction of Triticum aestivum cv. Highbury was shown to react with related subunits from other cultivars of wheat. The reaction was measured quantitatively by laser nephelometry in polyethylene glycol phosphate-buffered saline after dissolving the HMW fraction in 0.1 M acetic acid; urea used to dissolve the HMW prolamins inhibited the reaction, in some cases at the low concentration of 0.06 M. A study of the comparative reactions of other cereal prolamins was made. 'D' hordein, the homologous HMW protein of barley, showed less reaction, which was more inhibited by urea than the wheat subunits. Some ω-gliadins from the wheat cultivars Chinese Spring and Cheyenne reacted more strongly than the injected fraction and there was less inhibition by urea. A-, β- and γ3 of wheat also reacted with the antiserum while a secalin of rye of Mr 40000 gave a weak reaction.

Immunochemical studies on barley seed storage proteins : The specificity of an antibody to 'C' hordein and its reaction with prolamins from other cereals

The antigenic relationships between the prolamins of barley, rye and wheat have been studied by examining the specificity of an antibody to 'C' hordein in a quantitative study using a laser nephelometer. The antibody reacts weakly with 'B' hordein and strongly with 75-kdalton and 40-kdalton γ-secalins from rye and γ3 some ω-gliadins from wheat. Absorption experiments and immunodiffusion tests indicate that there are shared antigenic determinants for most of the prolamins. All the species with reacting prolamins belong to the sub-family Festucoideae of the Gramineae. The prolamins of maize, pearl millet and sorghum, species of the sub-family Panicoideae, do not react. The results confirm the known lack of homology between the prolamins of the two sub-families and also indicate the presence of relationships not yet established between 'C' hordein, the 75-kdalton and 40-kdalton γ-secalins and also γ3 gliadin.

Hordein-gene expression during development of the barley (Hordeum vulgare) endosperm

A previous study [Rahman, Shewry & Miflin (1982) J. Exp. Bot. 33, 717-728] showed differential accumulation of the major storage proteins (called B and C hordeins) in developing endosperms of barley (Hordeum vulgare). To determine how this accumulation is regulated, we have studied mRNA fractions prepared from similar endosperms. Hordein-related mRNA species were detected some days before the deposition of hordeins in vivo. The translation products in vivo directed by polyribosomes, polysomal RNA and total cellular RNA showed similar changes in the proportions of the hordein products to those observed in the accumulations of the proteins in vivo. There was a relative increase in one of the subfamilies of B hordeins (called B1 hordein) and a decrease in the second subfamily of B hordeins (B3 hordein) and in C hordeins. The populations of RNA species related to these three groups of hordeins were studied by 'dot hybridization', with specific complementary-DNA probes for B1-, B3- and C-hordein-related sequences. This showed a 10-15-fold increase in sequences related to the B1 hordein during endosperm development, but only a 4-fold increase in sequences related to B3 and C hordeins. These results indicate that the rates of synthesis of hordeins are related to the abundance of their respective mRNA species. The different results observed for the two subfamilies of B hordeins are of interest, since they indicate differential expression of two subfamilies of genes present at a single multigenic locus.