Primary structure of a C-hordein gene from barley

Immunolocalization of hordein synthesis and transport in developing barley endosperm

The spatial accumulation of hordeins in the developing endosperm of barley grains was examined by immunofluorescence microscopy (immunolight microscopy [iLM]) and immunoelectron microscopy (iEM) to establish the timing and subcellular pattern of hordein synthesis and deposition. The pattern seen for hordeins was compared to other abundant grain proteins, such as serpin Z4 and lipid transfer protein 1 (LTP1). Hordein accumulates throughout grain development, from 6 to 37 days post-anthesis (DPA). In contrast, serpin Z4 was present at 6 DPA, but the greatest synthesis and accumulation occurred during the middle of seed development, from 15 to 30 DPA. LTP1 accumulated later in seed development, from 15 to 30 DPA. Hordeins accumulated within the lumen of the endoplasmic reticulum (ER), were exocytosed from the ER membrane, and accumulated in protein bodies, which then fused either with the protein storage vacuoles or with other protein bodies, which also later fused with the protein storage vacuoles. iEM showed hordein, and LTP1 appeared not to traverse the Golgi apparatus (GA). Hordein, LTP1, and serpin Z4 colocalized to the same protein bodies and were co-transported to the protein storage vacuole in the same protein bodies. It is likely that this represents a general transport mechanism common to storage proteins in developing grains.

The association between hordein polypeptide banding and agronomic traits in partitioning genetic diversity in six-rowed Ethiopian barley lines (Hordeum vulgare L.)

BACKGROUND

Evaluation of the extent of genetic variation within and between the populations of crop genetic resources are of paramount importance in any breeding program. An experiment aimed at assessing the extent of variation among barley lines and the degree of association between hordein polypeptide and agronomic traits was hence executed.

METHODS

Field experiment was conducted in six environments between 2017-2019 involving 19 barley lines. Hordein bands were separated using vertical Sodium Dodecyl Sulphate Poly- acrylamide Gel Electrophoresis (SDS-PAGE).

RESULTS

The analysis of variance revealed significant variation among lines and wider range units were observed for the agronomic traits. The line (Acc# 16,811-6) was superior, producing the highest grain yield (2.97 ton ha^-1) across environments, 3.6 ton ha^-1 at Holleta, and 1.93 ton ha^-1 at Chefedonsa. At Arsi Negelle a different line Acc# 17146-9 was the highest yielding (3.15ton ha^-1). SDS-PAGE-based analysis of barley lines separated 12 hordein bands between C (four bands) and B (eight bands) subunits. Interestingly bands 52, 46a, and 46b were uniquely conserved in the four naked barley lines (Acc#16809-14,16956-11, 17240-3, 17244-19). A considerably high proportion of genetic diversity within the populations than among the populations could be a repercussion of high gene flow which substantiates the longstanding and dominant informal seed exchange system among the farmers. The significant positive association between grain yield and band 50 evocates the expression of this allele may code for higher grain yield. The negative association between days to maturity and band 52 perhaps stipulates earliness in barely lines upon the manifestation of the band. Band 52 and 60 appeared to be associated with more than one agronomic trait (days to maturity and thousand kernel weight; grain filling period and grain yield respectively) and could be the result of pleiotropic characteristics of the genes residing in these banding regions.

CONCLUSION

The barley lines exhibited substantial variation for hordein protein and agronomic traits. However, imparted the need for the implementation of decentralized breeding as a consequence of genotype-by-environment interaction. Significant hordein polypeptide and agronomic traits association advocated the utilization of hordein as a protein marker and perhaps consider them in the parental line selection.

From analysis of mutants to genetic engineering

This chapter describes the research of developing transgenic barley for synthesis of recombinant proteins with practical significance and of metabolic engineering of proanthocyanidin-free barley. The results were obtained by graduate students, postdoctoral researchers, and visiting scientists at the Carlsberg Laboratory from 1972-1996 and during the past ten years at Washington State University. It is written in appreciation of their enthusiasm, skill, and perseverance.

Similarities of omega gliadins from Triticum urartu to those encoded on chromosome 1A of hexaploid wheat and evidence for their post-translational processing

The omega-gliadins encoded on chromosome 1 of the A genome were purified from Triticum aestivum L. (2n=6 x=42, AABBDD) cv. Butte86, nullisomic 1D-tetrasomic 1A of cv. Chinese Spring (CS N1DT1A), and the diploid T. urartu (2n=2 x=14, AA ). Reverse-phase high-performance liquid chromatography combined with sodium dodecyl sulfate-polyacrylamide gel electrophoresis of gliadin extracts from CS nullisomic-tetrasomic (NT) lines confirmed the assignment to chromosome 1A. The purified omega-gliadins were characterized by mass spectrometry and N-terminal sequencing. The 1A-encoded omega-gliadins were smaller than 1B- or 1D-encoded omega-gliadins. The N-terminal amino acid sequences for 1A omega-gliadin mature peptides were nearly identical to those for the T. urartu omega-gliadins and were more similar to 1D omega-gliadin sequences than to sequences for T. monococum omega-gliadins, barley C-hordeins, or rye omega-secalins. They diverged greatly from the N-terminal sequences for the 1B omega-gliadins. The data suggest that T. urartu is the A-genome donor, and that post-translational cleavage by an asparaginyl endoprotease produces those omega-gliadins with N-terminal sequences beginning with KEL.

Substrate specificity of barley cysteine endoproteases EP-A and EP-B

The cysteine endoproteases (EP)-A and EP-B were purified from green barley (Hordeum vulgare L.) malt, and their identity was confirmed by N-terminal amino acid sequencing. EP-B cleavage sites in recombinant type-C hordein were determined by N-terminal amino acid sequencing of the cleavage products, and were used to design internally quenched, fluorogenic peptide substrates. Tetrapeptide substrates of the general formula 2-aminobenzoyl-P2-P1-P1'-P2'-tyrosine(NO2)-aspartic acid, in which cleavage occurs between P1 and P1', showed that the cysteine EPs preferred phenylalanine, leucine, or valine at P2. Arginine was preferred to glutamine at P1, whereas proline at P2, P1, or P1' greatly reduced substrate kinetic specificity. Enzyme cleavage of C hordein was mainly determined by the primary sequence at the cleavage site, because elongation of substrates, based on the C hordein sequence, did not make them more suitable substrates. Site-directed mutagenesis of C hordein, in which serine or proline replaced leucine, destroyed primary cleavage sites. EP-A and EP-B were both more active than papain, mostly because of their much lower Km values.

Detection of the Sec-1 locus of rye by a PCR-based method

The structural genes for the omega-secalins of rye (Secale cereale) are located in the Sec-1 locus on the short arm of rye chromosome 1R. We applied PCR (polymerase chain reaction) to detect the Sec-1 locus in a wheat genomic background. A primer set we designed based on a published sequence of a omega-secalin gene amplified not only the omega-secalin sequence, but also a putative omega-gliadin sequence. We determined partial sequences of both PCR-amplified fragments and designed different primers for the specific amplification of the omega-secalin sequence. One of the new primer sets amplified DNA fragments only in rye and wheat lines carrying chromosome 1R or telosome 1RS; no amplification occurred in either euploid wheats or 1RS deletion lines. This PCR-based method would provide efficient screening for the Sec-1 locus in progeny of wheat lines carrying chromosome 1R.

Isolation and promoter characterization of barley gene Itr1 encoding trypsin inhibitor BTI-CMe: differential activity in wild-type and mutant lys3a endosperm

The gene Itr1, encoding trypsin inhibitor BTI-CMe, has been obtained from a genomic library of Hordeum vulgare L. The gene has no introns and presents in its 5'-upstream region 605 bp that are homologous to the long terminal repeats (LTR) of the 'copia-like' retro-transposon Bare-1. Functional analysis of the Itr1 promoter by transient expression in protoplasts derived from different barley tissues, has shown that in this system the Itr1 promoter retains its endosperm specifity and the trans-regulation mediated by the Lys3a gene. The proximal promoter extending 343 bp upstream of the translation initiation ATG codon is sufficient to confer full GUS expression and for endosperm specifity. In protoplasts derived from the lys3a mutant, Risø 1508, GUS activity was less than 5% of that obtained with the same constructs in the protoplasts of wild-type Bomi from which it derives. Gel retardation experiments, after incubation with proteins obtained from both types of endosperm nuclei, also show differential patterns. Possible reasons for these differences are discussed.

Hordein promoter methylation and transcriptional activity in wild-type and mutant barley endosperm

B- and C-hordein gene transcription is severely reduced in the endosperm of the regulatory barley mutant lys3a, and this is correlated with persistent hypermethylation of the promoters. In contrast, D-hordein is expressed at normal levels in the mutant. To confirm the connection between methylation and transcriptional activity, a genomic D-hordein clone was isolated and sequenced. The nucleotide composition of the promoter region revealed a CpG island and methylation analysis, using bisulphite treatment of genomic DNA, confirmed that the D-hordein promoter is unmethylated in endosperm and leaf tissue. Immunocytochemical studies localized D-hordein to the reticular component of protein bodies in both the wild-type Bomi and lys3a. Transient expression of GUS reporter gene constructs in barley endosperm, following transfection by particle bombardment revealed the D-hordein promotors. Comparison of transient expression in Bomi and lys3a endosperm demonstrated that the activities of the unmethylated D-hordein and the Hor1-14 C-hordein promoters were equivalent, while the activities in the mutant of the Horl-17 C-hordein and the Hor2-4 B-hordein promoters were reduced two- and tenfold, respectively. Methylation of plasmids in vitro prior to expression severely inhibited B- and D-hordein promoter activities. Based on these observations two categories of promoters for endosperm-specific expression of storage proteins are recognized and a model involving methylation and modulation of chromatin structure in the regulation by the Lys3 gene is presented.

The relationship between physical and genetic distances at the Hor1 and Hor2 loci of barley estimated by two-colour fluorescent in situ hybridization

The hordeins are the major class of storage proteins in barley. They are encoded by multigene families. The B- and C-hordein loci have been mapped physically to the distal end of chromosome 5 (1I) of cultivated barley by fluorescent in situ hybridization. Based on measurements of chromosomal distances between the two hordein loci, the relationship between genetic and physical distances has been estimated to be about 1 mega base pairs per centiMorgan. This is four times higher than the mean value for the barley genome as a whole and confirms the tendency to increased recombination in distal chromosome regions. The resolving power of two-colour FISH is discussed. It is concluded that the method is suitable for estimating the relationship between genetic and physical distances of regions of about 10 Mbp or larger.

Sequence of a 28.6 kb region of yeast chromosome XI includes the FBA1 and TOA2 genes, an open reading frame (ORF) similar to a translationally controlled tumour protein, one ORF containing motifs also found in plant storage proteins and 13 ORFs with weak or no homology to known proteins

The complete DNA sequence of cosmid clone pUKG148 comprising 28,600 base pairs was determined from an ordered set of subclones. The sequence contains 22 open reading frames longer than 100 amino acids of which five are entirely covered by other, longer reading frames. YKL054 exhibits 25% homology at the amino acid level to a number of plant storage proteins of the glutenin type, YKL056 is 40% homologous to a translationally controlled mammalian tumour protein, YKL058 (TOA2) is identical to the small subunit of transcription factor TFIIA from yeast and YKL060 is identical to the FBA1 gene also from yeast, already sequenced but not mapped to chromosome XI. The remaining 13 open reading frames show weak or no homology to known genes.

Analysis of nuclear proteins interacting with a wheat alpha/beta-gliadin seed storage protein gene

The promoter region (-524 to -46) of the wheat alpha/beta-gliadin seed storage protein gene was analyzed for interactions with nuclear proteins from developing wheat seeds. Six complexes were detected within the first 165 bp upstream of the transcriptional start site. One of the proteins was a non-sequence specific AT-binding protein. The remaining five proteins bound in a sequence specific manner. One (CABP) mapped to a conserved CA-rich element at -134 to -112 while another (PalBP) mapped to an adjacent, palindromic sequence at -112 to -106. Three proteins (CTBPs 1-3) formed complexes at two, independent homologous sites. The activities of four of the binding proteins, CTBPs 1-3 and CABP, exhibited similar patterns of expression during seed development: they first appeared at early to mid stages, reached a maximum at mid stage and subsequently decreased, paralleling the pattern of gliadin mRNA accumulation. The non-specific AT-binding protein was detected at relatively high levels only at mid development. PalBP activity, on the other hand, first appeared at mid stage and was present at a constant level throughout later stages of development. The results suggest that the binding proteins may regulate gliadin expression in an antagonistic manner.

Small-angle X-ray-scattering studies of the C hordeins of barley (Hordeum vulgare)

Small angle X-ray scattering was used to study the solution conformation of the C hordeins of barley (Hordeum vulgare), a group of proteins whose primary structure consists predominantly of an octapeptide repeat motif. Measurements on the protein in 0.1 M-acetic acid at 25 degrees C are consistent with a model for the protein conformation of a stiff coil, the so-called 'worm-like' chain. The characteristic parameters (the Kuhn statistical segment length and the contour length) of the protein were calculated as 5.11 and 71.5 nm respectively.

A plant serpin gene. Structure, organization and expression of the gene encoding barley protein Z4

A 3133-bp nucleotide sequence of the gene Paz1 on chromosome 4 of barley, encoding endosperm protein Z4, has been determined. The sequence includes 1079 bp 5' upstream and 523 bp 3' downstream of the coding region. The 1079-bp 5' upstream region of the gene shows little similarity to 5' regions of other sequences genes expressed in the developing cereal endosperm. The coding sequence is interrupted by one 334-bp-long intron (bases 1497-1830). The deduced amino acid sequence, which was corroborated by peptide sequences, consists of 399 amino acids and has a molecular mass of 43,128 Da. This sequence confirms protein Z4 to be a member of the serpin superfamily of proteins. The similarity with other members of the family expressed as amino acids in identical positions is in the order of 25-30% and pronounced in the carboxy-terminal half of the molecule. Sequence residues assumed to form clusters stabilizing the tertiary structure are highly conserved. Protein Z4 is synthesized in the developing endosperm without a signal peptide and protein Z4 mRNA was evenly distributed among the free and membrane-bound polyribosomes of the endosperm cell. An internal hydrophobic region of 21 amino acids (residues 36-56) may serve as a signal for targeting the polypeptide into the lumen of the endoplasmic reticulum. The gene for protein Z4 could not be detected in the barley variety Maskin and some of its descendants. The 'high-lysine' allees, lys1 (Hiproly barley) and lys3a (Bomi mutant 1508) on chromosome 7, enhance and repress, respectively, the expression of the protein Z4 gene. Also, 1554 bp of another 8-kbp fragment of the barley genome Paz psi, similar to the protein-Z4-coding region, have been determined. Small insertions and deletions and the presence of an internal stop codon identify this fragment as part of a pseudogene related to the protein Z4 gene.

Conformational studies of a synthetic peptide corresponding to the repeat motif of C hordein

C hordein, a storage protein from barley grains, has an Mr of about 53,000, and consists predominantly of repeated octapeptides with a consensus sequence of Pro-Gln-Gln-Pro-Phe-Pro-Gln-Gln. Previously reported hydrodynamic and c.d. studies indicate the presence of beta-turns, the repetitive nature of which may lead to the formation of a loose spiral. In order to study these turns we have compared the structures of a synthetic peptide corresponding to the consensus repeat motif and total C hordein by using c.d. and Fourier-transform i.r. spectroscopy. The synthetic peptide exhibited spectra typical of beta I/III reverse turns when dissolved in trifluoroethanol at 22 degrees C and in water at 70 degrees C, but 'random-coil'-like spectra in water at 22 degrees C. The whole protein also showed increases in beta I/III reverse turns when dissolved in increasing concentrations of trifluoroethanol (50-100%, v/v) or heated in ethanol/water (7:3, v/v). Two cryogenic solvent systems were used to determine the c.d. spectra of the peptide and protein at temperatures down to -100 degrees C. Methanol/glycerol (9:1, v/v) and ethanediol/water (2:1, v/v) were selected as analogues of trifluoroethanol/water and water respectively. The peptide exhibited beta I/III-reverse-turn and 'random-coil'-like spectra in methanol/glycerol and ethanediol/water respectively at 22 degrees C, but a spectrum similar to that of a poly-L-proline II helix in both solvents at -100 degrees C. Similarly the proportion of this spectral type also increased when the whole protein was cooled in both solvents. These results indicate that a poly-L-proline II conformation at low temperatures is in equilibrium with a beta I/III-turn-rich conformation at higher temperatures. The latter conformation is also favoured in solvents of low dielectric constant such as trifluoroethanol. The 'random-coil'-like spectra exhibited by the protein and peptide in high-dielectric-constant solvents at room temperature may result from a mixture of the two conformations rather than from the random-coil state.

Molecular characterization of an active wheat LMW glutenin gene and its relation to other wheat and barley prolamin genes

The isolation and characterisation by DNA sequencing of a low molecular weight (LMW) glutenin gene from wheat is described. The deduced protein contains a signal peptide, a central repetitive region rich in proline and glutamine and N and C terminal non-repetitive domains, similar to other prolamins. A detailed comparison of the C terminal domain of 20 prolamin genes enabled us to divide them into 4 families. The LMW glutenin family is distinct from the alpha, beta- and gamma-gliadin families of wheat and is closest to the B hordein genes of barley. This and other comparisons were also used to assess the pattern of genetic variation among prolamin sequences and to provide a molecular basis for the interpretation of prolamin size polymorphism. The 5' flanking fragment of the isolated gene was previously shown to direct endosperm-specific expression of a reporter gene in transgenic tobacco. Evidence is provided that the isolated gene is also active in wheat and its transcription initiation site was determined. Features of the gene which may be relevant to its activity are discussed.

A γ-hordein gene

The 1614 bp nucleotide sequence of a barley gene encoding a γ-hordein endosperm storage polypeptide is presented. The deduced amino acid sequence is 305 amino acids long. It comprises a 19 amino acid signal peptide, an N-terminal half composed of proline-glutamine blocks organized in repeating units and a C-terminal half where the repeats are dispersed and less conserved. The deduced amino acid sequence shows strong homology to a γ-gliadin polypeptide from wheat and a γ-secalin polypeptide from rye and less homology to a B1 hordein polypeptide from barley. The 378 bp 5' non-coding region contains a TATA box at-85, an AGGA sequence at-105 and a-300 element typical of prolamin storage protein genes. The transcript start is 56 bp upstream of the ATG codon and 30 bp downstream of the TATA box. The 318 bp 3' non-coding region contains 2 putative polyadenylation signals, 76 and 132 bp downstream of the stop codon. γ-Hordein polypeptides are encoded by a small multigene family. The γ-hordein gene family is not part of the deleted chromosome 5 region, containing the Hor 2 locus, in the B hordein-deficient mutant hor 2ca. Two mRNA size classes of 1350 and 1450 nt are detectable in wild-type endosperms from 8 to 26 days after anthesis. The mutant hor 2ca contains as much γ-hordein mRNA as the wild type, whereas the B and C hordein-deficient mutant lys 3a contains barely detectable amounts.