Barley alpha-amylase genes. Quantitative comparison of steady-state mRNA levels from individual members of the two different families expressed in aleurone cells

Structural organization and functional divergence of high isoelectric point α-amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

BACKGROUND

High isoelectric point α-amylase genes (Amy1) play major roles during cereal seed germination, and are associated with unacceptable high residual α-amylase activities in ripe wheat grains. However, in wheat and barley, due to extremely high homology of duplicated copies, and large and complex genome background, the knowledge on this multigene family is limited.

RESULTS

In the present work, we identified a total of 41 Amy1 genes among 13 investigated grasses. By using genomic resources and experimental validation, the exact copy numbers and chromosomal locations in wheat and barley were determined. Phylogenetic and syntenic analyses revealed tandem gene duplication and chromosomal rearrangement leading to separation of Amy1 into two distinct loci, Amy1θ and Amy1λ. The divergence of Amy1λ from Amy1θ was driven by adaptive selection pressures performed on two amino acids, Arg97 and Asn233 (P > 0.95*). The predicted protein structural alteration caused by substitution of Asp233Asn in the conserved starch binding surface site, and significantly expressional differentiation during seed germination and grain development provided evidence of functional divergence between Amy1θ and Amy1λ genes. We screened out candidate copies (TaAmy1-A1/A2 and TaAmy1-D1) associated with high residual α-amylase activities in ripe grains. Furthermore, we proposed an evolutionary model for expansion dynamics of Amy1 genes.

CONCLUSIONS

Our study provides comprehensive analyses of the Amy1 multigene family, and defines the fixation of two spatially structural Amy1 loci in wheat and barley. Potential functional divergence between them is reflected by their sequence features and expressional patterns, and driven by gene duplication, chromosome rearrangement and natural selections during gene family evolution. Furthermore, the discrimination of differentially effective copies during seed germination and/or grain development will provide guidance to manipulation of α-amylase activity in wheat and barley breeding for better yield and processing properties.

Comparisons of Copy Number, Genomic Structure, and Conserved Motifs for α-Amylase Genes from Barley, Rice, and Wheat

Barley is an important crop for the production of malt and beer. However, crops such as rice and wheat are rarely used for malting. α-amylase is the key enzyme that degrades starch during malting. In this study, we compared the genomic properties, gene copies, and conserved promoter motifs of α-amylase genes in barley, rice, and wheat. In all three crops, α-amylase consists of four subfamilies designated amy1, amy2, amy3, and amy4. In wheat and barley, members of amy1 and amy2 genes are localized on chromosomes 6 and 7, respectively. In rice, members of amy1 genes are found on chromosomes 1 and 2, and amy2 genes on chromosome 6. The barley genome has six amy1 members and three amy2 members. The wheat B genome contains four amy1 members and three amy2 members, while the rice genome has three amy1 members and one amy2 member. The B genome has mostly amy1 and amy2 members among the three wheat genomes. Amy1 promoters from all three crop genomes contain a GA-responsive complex consisting of a GA-responsive element (CAATAAA), pyrimidine box (CCTTTT) and TATCCAT/C box. This study has shown that amy1 and amy2 from both wheat and barley have similar genomic properties, including exon/intron structures and GA-responsive elements on promoters, but these differ in rice. Like barley, wheat should have sufficient amy activity to degrade starch completely during malting. Other factors, such as high protein with haze issues and the lack of husk causing Lauting difficulty, may limit the use of wheat for brewing.

Synthetic promoters in planta

This paper reviews the importance, prospective and development of synthetic promoters reported in planta. A review of the synthetic promoters developed in planta would help researchers utilize the available resources and design new promoters to benefit fundamental research and agricultural applications. The demand for promoters for the improvement and application of transgenic techniques in research and agricultural production is increasing. Native/naturally occurring promoters have some limitations in terms of their induction conditions, transcription efficiency and size. The strength and specificity of native promoter can be tailored by manipulating its 'cis-architecture' by the use of several recombinant DNA technologies. Newly derived chimeric promoters with specific attributes are emerging as an efficient tool for plant molecular biology. In the last three decades, synthetic promoters have been used to regulate plant gene expression. To better understand synthetic promoters, in this article, we reviewed promoter structure, the scope of cis-engineering, strategies for their development, their importance in plant biology and the total number of such promoters (188) developed in planta to date; we then categorized them under different functional regimes as biotic stress-inducible, abiotic stress-inducible, light-responsive, chemical-inducible, hormone-inducible, constitutive and tissue-specific. Furthermore, we identified a set of 36 synthetic promoters that control multiple types of expression in planta. Additionally, we illustrated the differences between native and synthetic promoters and among different synthetic promoter in each group, especially in terms of efficiency and induction conditions. As a prospective of this review, the use of ideal synthetic promoters is one of the prime requirements for generating transgenic plants suitable for promoting sustainable agriculture and plant molecular farming.

Spatiotemporal profiling of starch biosynthesis and degradation in the developing barley grain

Barley (Hordeum vulgare) grains synthesize starch as the main storage compound. However, some starch is degraded already during caryopsis development. We studied temporal and spatial expression patterns of genes coding for enzymes of starch synthesis and degradation. These profiles coupled with measurements of selected enzyme activities and metabolites have allowed us to propose a role for starch degradation in maternal and filial tissues of developing grains. Early maternal pericarp functions as a major short-term starch storage tissue, possibly ensuring sink strength of the young caryopsis. Gene expression patterns and enzyme activities suggest two different pathways for starch degradation in maternal tissues. One pathway possibly occurs via alpha-amylases 1 and 4 and beta-amylase 1 in pericarp, nucellus, and nucellar projection, tissues that undergo programmed cell death. Another pathway is deducted for living pericarp and chlorenchyma cells, where transient starch breakdown correlates with expression of chloroplast-localized beta-amylases 5, 6, and 7, glucan, water dikinase 1, phosphoglucan, water dikinase, isoamylase 3, and disproportionating enzyme. The suite of genes involved in starch synthesis in filial starchy endosperm is much more complex than in pericarp and involves several endosperm-specific genes. Transient starch turnover occurs in transfer cells, ensuring the maintenance of sink strength in filial tissues and the reallocation of sugars into more proximal regions of the starchy endosperm. Starch is temporally accumulated also in aleurone cells, where it is degraded during the seed filling period, to be replaced by storage proteins and lipids.

Spatio-temporal profiling and degradation of α-amylase isozymes during barley seed germination

Ten genes from two multigene families encode barley alpha-amylases. To gain insight into the occurrence and fate of individual isoforms during seed germination, the alpha-amylase repertoire was mapped by using a proteomics approach consisting of 2D gel electrophoresis, western blotting, and mass spectrometry. Mass spectrometric analysis confirmed that the 29 alpha-amylase positive 2D gel spots contained products of one (GenBank accession gi|113765) and two (gi|4699831 and gi|166985) genes encoding alpha-amylase 1 and 2, respectively, but lacked products from seven other genes. Eleven spots were identified only by immunostaining. Mass spectrometry identified 12 full-length forms and 12 fragments from the cultivar Barke. Products of both alpha-amylase 2 entries co-migrated in five full-length and one fragment spot. The alpha-amylase abundance and the number of fragments increased during germination. Assessing the fragment minimum chain length by peptide mass fingerprinting suggested that alpha-amylase 2 (gi|4699831) initially was cleaved just prior to domain B that protrudes from the (betaalpha)(8)-barrel between beta-strand 3 and alpha-helix 3, followed by cleavage on the C-terminal side of domain B and near the C-terminus. Only two shorter fragments were identified of the other alpha-amylase 2 (gi|166985). The 2D gels of dissected tissues showed alpha-amylase degradation to be confined to endosperm. In contrast, the aleurone layer contained essentially only full-length alpha-amylase forms. While only products of the above three genes appeared by germination also of 15 other barley cultivars, the cultivars had distinct repertoires of charge and molecular mass variant forms. These patterns appeared not to be correlated with malt quality.

Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique

The primary objective of this study was to elucidate gene organization and to integrate the genetic linkage map for barley (Hordeum vulgare L.) with a physical map using ultrasensitive fluorescence in situ hybridization (FISH) techniques for detecting signals from restriction fragment length polymorphism (RFLP) clones. In the process, a single landmark plasmid, p18S5Shor, was constructed that identified and oriented all seven of the chromosome pairs. Plasmid p18S5Shor was used in all hybridizations. Fourteen cDNA probes selected from the linkage map for barley H. vulgare 'Steptoe' x H. vulgare 'Morex' (Kleinhofs et al. 1993) were mapped using an indirect tyramide signal amplification technique and assigned to a physical location on one or more chromosomes. The haploid barley genome is large and a complete physical map of the genome is not yet available; however, it was possible to integrate the linkage map and the physical locations of these cDNAs. An estimate of the ratio of base pairs to centimorgans was an average of 1.5 Mb/cM in the distal portions of the chromosome arms and 89 Mb/cM near the centromere. Furthermore, while it appears that the current linkage maps are well covered with markers along the length of each arm, the physical map showed that there are large areas of the genome that have yet to be mapped.

T-DNA integration into the barley genome from single and double cassette vectors

Patterns and sites of T-DNA integrations into the barley genome from single and double cassette vectors are of interest for the identification of cultivars with value added properties as well as for the production of selection marker-free transgenic lines that can be retransformed. T-DNA/Plant DNA junctions were obtained by capturing a single-stranded DNA with a biotinylated primer annealing to the vector adjacent to the border and an adaptor ligated to a restriction site overhang in the flanking barley DNA. The captured junction was converted into a double strand and sequenced. Fifty left and right border junctions from plants transgenic for one of five human genes were analyzed. Primers of 15-30 nucleotides designed from the genomic DNA at the insertion site can PCR amplify fragments that identify unequivocally any transformant. Adjacent transgene insertions with single cassette vectors were always in tandem direct repeat configuration. With regard to T-DNA integration the patterns were comparable to the variations found in dicotyledonous plants. Twelve of the 46 integrations characterized by blast searches were within different regions of the BARE-1 retrotransposon element occurring with a frequency of 2 x 10(5) copies in the barley genome. The use of border junctions to identify number of copies and loci of integrates in transformants is discussed.

Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation

alpha-Amylase 2 (AMY2) and alpha-amylase/subtilisin inhibitor (BASI) from barley bind with Ki = 0.22 nM. AMY2 is a (beta/alpha)8-barrel enzyme and the segment Leu116-Phe143 in domain B (Val89-Ile152), protruding at beta-strand 3 of the (beta/alpha)8-barrel, was shown using isozyme hybrids to be crucial for the specificity of the inhibitor for AMY2. In the AMY2-BASI crystal structure [F. Vallée, A. Kadziola, Y. Bourne, M. Juy, K. W. Rodenburg, B. Svensson & R. Haser (1998) Structure 6, 649-659] Arg128AMY2 forms a hydrogen bond with Ser77BASI, while Asp142AMY2 makes a salt-bridge with Lys140BASI. These two enzyme residues are substituted by glutamine and asparagine, respectively, to assess their contribution in binding of the inhibitor. These mutations were performed in the well-expressed, inhibitor-sensitive hybrid barley alpha-amylase 1 (AMY1)-(1-90)/AMY2-(90-403) with Ki = 0.33 nM, because of poor production of AMY2 in yeast. In addition Arg128, only found in AMY2, was introduced into an AMY1 context by the mutation T129R/K130P in the inhibitor-insensitive hybrid AMY1-(1-161)/AMY2-(161-403). The binding energy was reduced by 2.7-3.0 kcal.mol-1 as determined from Ki after the mutations R128Q and D142N. This corresponds to loss of a charged interaction between the protein molecules. In contrast, sensitivity to the inhibitor was gained (Ki = 7 microM) by the mutation T129R/K130P in the insensitive isozyme hybrid. Charge screening raised Ki 14-20-fold for this latter mutant, AMY2, and the sensitive isozyme hybrid, but only twofold for the R128Q and D142N mutants. Thus electrostatic stabilization was effectively introduced and lost in the different mutant enzyme-inhibitor complexes and rational engineering using an inhibitor recognition motif to confer binding to the inhibitor mimicking the natural AMY2-BASI complex.

Signaling from the embryo conditions Vp1-mediated repression of alpha-amylase genes in the aleurone of developing maize seeds

The VP1 transcription factor functions as both a repressor and an activator of gene expression in the developing aleurone. Vp1 activation of the anthocyanin pathway exhibits strict cell autonomy in aleurone. In contrast, Vp1-mediated repression of hydrolase genes in aleurone cells during seed development is determined by a combination of cell autonomous and cell non-autonomous signals. To analyze signaling between the embryo and aleurone during seed development, a T-B3La chromosome translocation was used to create seed that has non-concordant embryo and endosperm genotypes. We show that de-repression of an Amy-GUS reporter gene in developing vp1 mutant aleurone cells strongly depends on the presence of a viviparous embryo. Genetic ablation of the developing embryo in vp1 mutant and Vp1 seeds through the introduction of an early embryo mutation caused a similar enhancement of Amy-GUS expression in the aleurone, suggesting that the quiescent embryo present in normal seed is a critical source of inhibitory signals. Analysis of an ABA deficient vp1 vp5 double mutant indicates that ABA synthesized in the embyro interacts additively with Vp1 to prevent precocious induction of alpha-amylase genes in the aleurone of the developing seed. A lack of ABA synthesis, however, does not account for the strongly synergistic interaction between a viviparous vp1 embryo and mutant aleurone suggesting that a quiescent embyro is a source of other inhibitory signals.

Cloning and characterization of a gibberellin-induced RNase expressed in barley aleurone cells

We cloned a cDNA for a gibberellin-induced ribonuclease (RNase) expressed in barley (Hordeum vulgare) aleurone and the gene for a second barley RNase expressed in leaf tissue. The protein encoded by the cDNA is unique among RNases described to date in that it contains a novel 23-amino acid insert between the C2 and C3 conserved sequences. Expression of the recombinant protein in tobacco (Nicotiana tabacum) suspension-cultured protoplasts gave an active RNase of the expected size, confirming the enzymatic activity of the protein. Analyses of hormone regulation of expression of mRNA for the aleurone RNase revealed that, like the pattern for alpha-amylase, mRNA levels increased in the presence of gibberellic acid, and its antagonist abscisic acid prevented this effect. Quantitative studies at early times demonstrated that cycloheximide treatment of aleurone layers increased mRNA levels 4-fold, whereas a combination of gibberellin plus cycloheximide treatment was required to increase alpha-amylase mRNA levels to the same extent. These results are consistent with loss of repression as an initial effect of gibberellic acid on transcription of those genes, although the regulatory pathways for the two genes may differ.

Mapping of the K(+)/Na (+) discrimination locus Kna1 in wheat

In saline environments, bread wheat, Triticum aestivum L. (genomes AABBDD), accumulates less Na(+) and more K(+) in expanding and young leaves than durum wheat, T. turgidum L. (genomes AABB). Higher K(+)/Na(+) ratios in leaves of bread wheat correlate with its higher salt tolerance. Chromosome 4D from bread wheat was shown in previous work to play an important role in the control of this trait and was recombined with chromosome 4B in the absence of the Ph1 locus. A population of plants disomic for 4D/4B recombined chromosomes in the genetic background of T. turgidum was developed to investigate the genetic control of K(+)/Na(+) discrimination by chromosome 4D. Evidence was obtained that the trait is controlled by a single locus, designated Kna1, in the long arm of chromosome 4D. In the present work, K(+)/Na(+) discrimination was determined for additional families with 4D/4B chromosomes. The concentrations of Na(+) and K(+)/Na(+) ratios in the youngest leaf blades clustered in two nonoverlapping classes, and all recombinant families could be unequivocally assigned to Kna1 and kna1 classes. The Kna1 locus scored this way was mapped on a short region in the 4DL arm and was completely linked to Xwg199, Xabc305, Xbcd.402, Xpsr567, and Xpsr375; it was also mapped as a quantitative trait. The results of the QTL analysis, based on the K(+)/Na(+) ratios in the young leaves of greenhousegrown plants and flag leaves of field-grown plants, agreed with the position of Knal determined as a qualitative trait. Several aspects of gene introgression by manipulation of the Ph1 locus are discussed.

Integrated control of seed maturation and germination programs by activator and repressor functions of Viviparous-1 of maize

The Viviparous-1 (VP1) transcriptional activator of maize is required for abscisic acid induction of maturation-specific genes late in seed development leading to acquisition of desiccation tolerance and arrest in embryo growth. Here, we show that VP1 also inhibits induction of the germination-specific alpha-amylase genes in aleurone cells of the developing seed and thereby appears to be involved in preventing precocious hydrolyzation of storage compounds accumulating in the endosperm. In developing seeds of the somatically instable vp1-m2 mutant, hydrolase activity was derepressed specifically in endosperm sectors underlying vp1 mutant aleurone. A barley alpha-amylase promoter-GUS reporter construct (Amy-GUS) was induced in developing vp1 mutant aleurone cells but not in wild-type aleurone cells. Moreover, transient expression of recombinant VP1 and vp1 mutant aleurone cells strongly inhibited expression of Amy-GUS and thus effectively complemented this aspect of the mutant phenotype. VP1 specifically repressed induction of Amy-GUS by the hormone gibberellic acid in aleurone of germinating barley seeds. Deletion of the acidic transcriptional activation domain of VP1 did not affect the inhibitory activity, indicating that VP1 has a discrete repressor function. Hence, physically combining activator and repressor functions in one protein may provide a mechanism to integrate the control of two normally consecutive developmental programs, seed maturation and seed germination.

Linkage relationships among stress-induced genes in wheat

Linkage relationships among genes responding to water-deficit, salt stress, and heat shock were investigated in diploid wheat, Triticum monococcum L. The position of these gene loci relative to closely linked markers and the centromeres is reported. It is proposed to continue to use the present T. monococcum mapping population and the genetic maps based thereon as a framework for future determination of relationships among other genes related to environmental stress in the tribe Triticeae.

Alternative polyadenylation generates three low-pI alpha-amylase mRNAs with differential expression in barley

Specific low-pI alpha-amylase genes from barley (Hordeum vulgare L.) produced alternative mRNAs with a 17-base 3' extension (extension 1) or a 17-base extension beyond this (extension 2). The extended mRNAs do not arise from splicing of downstream sequences, and not all low-pI genes contain the extended sequences. All three mRNAs occur in aleurones and shoots, while extension 2 is missing from scutella. Also, the unextended mRNAs predominate in total mRNA, but the extended mRNAs predominate in membrane-bound polysomes. The extended sequences do not occur in previously characterized alpha-amylases, but 16 of 18 bases, mainly in extension 1, are identical with a sequence in the 3'-UTR of PAPI, a putative inhibitor of alpha-amylase. These observations suggest that the extended sequences could play a functional role in alpha-amylase expression.

Polymorphisms in the α-amy1 gene of wild and cultivated barley revealed by the polymerase chain reaction

α-Amylases are the key enzymes involved in the hydrolysis of starch in plants. The polymerase chain reaction (PCR) was used to detect polymorphisms in the length of amplified sequences between the annealing sites of two primers derived from published α-amy1 gene sequences in barley. These two primers (Bsw1 and Bsw7), flanking the promoter region and the first exon, amplified two PCR fragments in barley. One of the amplified products, with the expected length of 820 bp, appeared together with another shorter PCR band of around 750 bp. This 750-bp fragment seems to be derived from an α-amylase gene not reported previously. Both of the PCR products could be amplified from the two-rowed barley varieties tested, including cv Himalaya from which the sequence information was obtained. Five of the six-rowed barley varieties also have the two PCR fragments whereas another two have only the long fragment. These two fragments seem to be unique to barley, neither of them could be amplified from other cereals; for example, wheat, rye or sorghum. These two α-amylase fragments were mapped to the long arm of 6H, the location of the α-amy1 genes, using wheat-barley addition lines. Amplification of genomic DNA from wild barley accessions with primers Bsw1 and Bsw7 indicated that both of the fragments could be present, or the long and short fragments could be present alone. The results also demonstrated that the genes specifying these two fragments could be independent from each other in barley. The conserved banding pattern of these two fragments in the two-rowed barley varieties implies that artificial selection from these genes may have played an important role in the evolution of cultivated barley from wild barley.

Quantitative trait locus effects and environmental interaction in a sample of North American barley germ plasm

Quantitative trait locus (QTL) and QTL x environment (E) interaction effects for agronomic and malting quality traits were measured using a 123-point linkage map and multi-environment phenotype data from an F1-derived doubled haploid population of barley (Hordeum vulgare). The QTL × E interactions were due to differences in magnitude of QTL effects. Highly significant QTL effects were found for all traits at multiple sites in the genome. Yield QTL peaks and support intervals often coincided with plant height and lodging QTL peaks and support intervals. QTL were detected in the vicinity of a previously mapped Mendelian maturity locus and known function probes forα- andβ-amylase genes. The average map density (9.6 cM) should be adequate for molecular marker-assisted selection, particularly since there were few cases of alternative favorable alleles for different traits mapping to the same or adjacent intervals.

Genetic polymorphisms of α- and β-amylase isozymes in wild emmer wheat, Triticum dicoccoides, in Israel

α- and β-amylase isozyme diversity was studied electrophoretically by thin-layer polyacrylamide gel isoelectrofocusing in the tetraploid wild emmer wheat, Triticum dicoccoides, the progenitor of all cultivated wheats. We analyzed 225 plants from 23 populations encompassing the ecological spectrum of T. dicoccoides in Israel. The results were as follows: (a) Band and multilocus genotype polymorphisms abound and vary within and between the four amylase components: malt, green (α-amylases), and dry and germinating seeds (β-amylases). (b) The number of bands of malt, green, and dry and germinating seeds were 20, 6, 11 and 13, respectively, generating 40, 6, 51, and 51 patterns or multilocus genotypes (MGP), respectively. The MGPs vary drastically within and between populations, from monomorphic in some populations with a single pattern to highly polymorphic ones, (c) Mean H e values for malt, green, and germinating and dry seeds are 0.053, 0.055, 0.088, and 0.077, respectively; mean number of bands per individual was 11.8, 4.4, 7.6, and 4.0, respectively, (d) The percentages of 50 bands and 148 multilocus genotype patterns (MGP) (in parenthesis) were classified into widespread, sporadic, and localized: 84.4 (10.8), 8.9 (12.2), 6.7 (77.0), respectively. Notably, 89.2% of the patterns were not widespread, but sporadic and localized, (e) The mean value of genetic distances among populations (Nei's D) for the four amylase groups is D = 0.136, 0.175, 0.288 and 0.307, respectively, not displaying geographical correlates. (f) Most of the α- and β-amylase diversity is between populations (G st = 68-75%). (g) Significant environmental correlates occur between either bands or patterns and climatic diversity (water and primarily temperature factors). (h) Significant associations of multilocus amylase bands occur across Israel. Like-wise, significant gametic phase disequilibria, D, occur within populations and are positively correlated with climatic variables, primarily that of temperature, (i) Discriminant analyses correctly classified (95-100%) the 23 wild emmer populations into their ecogeographical region and soil type. (j) Autocorrelation analysis showed that there is no correlation between bands and geographic distance and excluded migration as a major factor of amylase differentiation.These results suggest that diversifying climatic and edaphic natural selection rather than stochastisity or migration is the major evolutionary force driving amylase differentiation at both the single and multilocus levels. Furthermore, wild emmer harbors high levels of α- and β-amylase diversity both as single bands and as multilocus adaptive genetic patterns. These are exploitable both as genetic markers for quantitative loci (QTLs) and as adaptive genetic resources to improve wheat germination and growth through classical breeding and/or biotechnology.

Suppression of alpha-amylase gene expression by antisense oligodeoxynucleotide in barley cultured aleurone layers

Antisense oligodeoxynucleotides (ODNs) have been applied to regulate gene expression using cell-free media or animal cells. Here we demonstrate the specific inhibition of barley alpha-amylase gene expression by synthetic antisense ODNs. In a cell free system using wheat-germ extracts, 5 microM of a 20-mer antisense ODN prevented the synthesis of the polypeptide corresponding to the predetermined length of alpha-amylase translated in vitro, whereas there was no effect on other protein synthesis. Furthermore, in cultured aleurone cells, alpha-amylase activity was efficiently decreased by addition of ODNs. At the concentrations higher than 5 microM, antisense ODN inhibited alpha-amylase gene expression almost completely. These results imply that ODN could transport into the cultured aleurone cells crossing the cell membrane, and regulate specific gene expression. This simple model system could be applicable not only for the analysis of the alpha-amylase multigene family in barley but also for studying functions of cryptic genes in higher plant.

RAmy2A; a novel alpha-amylase-encoding gene in rice

The structure and expression of the alpha-amylase-encoding gene, RAmy2A, are described. This only representative of the Amy2 subfamily in rice differs from other cereal alpha-amylase-encoding genes in several respects. It contains the largest introns of all the cereal alpha-amylase-encoding genes examined to date. Moreover, the second of three introns in this gene contains a long inverted repeat sequence that can potentially form a large and stable stem-loop structure in the unspliced RNA transcript. Finally, RAmy2A is constitutively expressed at very low levels in germinated seeds, root, etiolated leaves, immature seeds and callus. This is in marked contrast to the Amy2 genes of wheat and barley which are highly expressed in the aleurone layer of the germinated seeds.

Primary structure of a novel barley gene differentially expressed in immature aleurone layers

As a direct approach to elucidate the molecular biology of barley aleurone cell development, we differentially screened an aleurone cDNA library made from poly(A)+ RNA of immature grains for clones representing transcripts present in the aleurone but not in the starchy endosperm. For one of these clones, B22E, which hybridies to a 0.7 kb transcript, Northern and in situ hybridization revealed that expression is under complex spatial, temporal and hormonal control in barley grains. cDNAs corresponding to B22E transcripts were isolated from aleurone/pericarp and embryo of developing grains, and from germinating scutella. Among these were the nearly full-length aleurone/pericarp clone pB22E.a16 (541 bp). cDNAs matching the sequence of this clone (type 1 transcript) were found for all tissues investigated. In addition, cDNAs with an extra 12 bp insertion (type 2 transcript) were obtained from germinating scutella. The two different transcripts can encode novel barley proteins of 115 and 119 amino acids, respectively. A gene designated B22EL8 was isolated and sequenced; it encodes the type 1 B22E transcript and contains two introns of 145 and 125 bp. Particle bombardment of barley aleurone with a B22EL8 promoter-GUS (beta-glucuronidase) construct demonstrates that the promoter (3 kb) is active in developing barley grains. The promoter is not, however, active in the seeds of tobacco plants transgenic for the B22EL8 gene, indicating the existence of sequences specific for monocots. A comparison of 1.4 kb of upstream sequence of B22E with the maize c1 promoter reveals a number of short, identical sequences which may be responsible for aleurone cell-specific gene transcription.

Chromosomal localization and genomic organization of α-amylase genes in rice (Oryza sativa L.)

Genes for α-amylase, alcohol dehydrogenase, andEm, an ABA-regulated gene expressed late in embryogenesis, were localized on rice chromosomes by the analysis of primary trisomies. The validity of the mapping approach was confirmed usingAdh-1 as a control. TheAdh-1 gene has previously been assigned to chromosome 11 using conventional techniques. In this study we confirm this assignment and report an additional locus for alcohol dehydrogenase (Adh-2) on chromosome 9. The α-amylase genes were located on chromosomes 1, 2, 6, 8, and 9 while theEm gene was mapped to chromosome 5. To facilitate trisomic analysis and correlation of cloned genes with bands observed on Southern blots, a nomenclature for the rice α-amylase genes has been proposed. In addition to mapping nine cloned α-amylase genes, we have identified two previously uncloned α-amylase genes as part of this study. Polymorphism for α-amylase genes belonging to each of the three subfamilies was observed between M202 and IR36. The maximum degree of polymorphism was found among genes belonging to the RAmy3 subfamily, which also has the most diverse group of genes.

Differential expression of alpha-amylase genes in germinating rice and barley seeds

Steady-state levels of mRNA from individual alpha-amylase genes were measured in the embryo and aleurone tissues of rice (Oryza sativa) and two varieties of barley (Hordeum vulgare L. cv. Himalaya and cv. Klages) during germination. Each member of the alpha-amylase multigene families of rice and barley was differentially expressed in each tissue. In rice, alpha-amylase genes displayed tissue-specific expression in which genes RAmy3B, RAmy3C, and RAmy3E were preferentially expressed in the aleurone layer, genes RAmy1A, RAmy1B and RAmy3D were expressed in both the embryo and aleurone, and genes RAmy3A and RAmy2A were not expressed in either tissue. Whenever two or more genes were expressed in any tissue, the rate of mRNA accumulation from each gene was unique. In contrast to rice, barley alpha-amylase gene expression was not tissue-specific. Messenger RNAs encoding low- and high-pI alpha-amylase isozymes were detectable in both the embryo and aleurone and accumulated at different rates in each tissue. In particular, peak levels of mRNA encoding high-pI alpha-amylases always preceded those encoding low-pI alpha-amylases. Two distinct differences in alpha-amylase gene expression were observed between the two barley varieties. Levels of high-pI alpha-amylase mRNA peaked two days earlier in Klages embryos than in Himalaya embryos. Throughout six days of germination, Klages produced three times as much high-pI alpha-amylase mRNA and nearly four times as much low-pI alpha-amylase mRNA than the slower-germinating Himalaya variety.

Control of transient expression of chimaeric genes by gibberellic acid and abscisic acid in protoplasts prepared from mature barley aleurone layers

Gibberellic acid (GA3) and abscisic acid (ABA) control the transcription of alpha-amylase genes in barley aleurone cells. This control is likely to be exerted through cis-acting hormone-responsive elements in the promoter region of the gene. In order to further define these elements, we have developed procedures for obtaining transient expression of chimaeric genes in protoplasts prepared from mature barley aleurone layers. Constructs with heterologous constitutive promoters and with heterologous and homologous GA3- and ABA-regulated promoters were expressed specifically by these cells. This system would appear to offer great potential in gene regulation studies especially for hormonally regulated homologous genes. Functional analysis of a barley alpha-amylase gene has been performed using this system. A 2050 bp fragment from a high-pI alpha-amylase gene was fused to a reporter gene (GUS) and control of its expression was examined. Deletion analysis of this promoter fragment showed that major GA- and ABA-responsive elements occurred between 174 and 41 bp upstream from the transcription initiation site.

Classification and characterization of the rice alpha-amylase multigene family

To establish the size and organization of the rice alpha-amylase multigene family, we have isolated 30 alpha-amylase clones from three independent genomic libraries. Partial characterization of these clones indicates that they fall into 5 hybridization groups containing a total of 10 genes. Two clones belonging to the Group 3 hybridization class have more than one gene per cloned fragment. The nucleotide sequence of one clone from Group 1, lambda OSg2, was determined and compared to other known cereal alpha-amylase sequences revealing that lambda OSg2 is the genomic analog of the rice cDNA clone, pOS103. The rice alpha-amylase genes in Group 1 are analogous to the alpha-Amy1 genes in barley and wheat. lambda OSg2 contains sequence motifs common to most actively transcribed genes in plants. Two consensus sequences, TAACAAGA and TATCCAT, were found in the 5' flanking regions of alpha-amylase genes of rice, barley and wheat. The former sequence may be specific to alpha-amylase gene while the latter sequence may be related to a 'CATC' box found in many plant genes. Another sequence called the pyrimidine box (TCCTTTTTC) was found in the alpha-amylase genes as well as other genes regulated by gibberellic acid (GA). Comparisons based on amino acid sequence alignment revealed that the multigene families in rice, barley and wheat shared a common ancestor which contained three introns. Some of the descendants of the progenitor alpha-amylase gene appear to have lost the middle intron while others maintain all three introns.