Molecular cloning and characterization of the Amylose-Extender gene encoding starch branching enzyme IIB in maize

A Systemic Investigation of Genetic Architecture and Gene Resources Controlling Kernel Size-Related Traits in Maize

Grain yield is the most critical and complex quantitative trait in maize. Kernel length (KL), kernel width (KW), kernel thickness (KT) and hundred-kernel weight (HKW) associated with kernel size are essential components of yield-related traits in maize. With the extensive use of quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) analyses, thousands of QTLs and quantitative trait nucleotides (QTNs) have been discovered for controlling these traits. However, only some of them have been cloned and successfully utilized in breeding programs. In this study, we exhaustively collected reported genes, QTLs and QTNs associated with the four traits, performed cluster identification of QTLs and QTNs, then combined QTL and QTN clusters to detect consensus hotspot regions. In total, 31 hotspots were identified for kernel size-related traits. Their candidate genes were predicted to be related to well-known pathways regulating the kernel developmental process. The identified hotspots can be further explored for fine mapping and candidate gene validation. Finally, we provided a strategy for high yield and quality maize. This study will not only facilitate causal genes cloning, but also guide the breeding practice for maize.

Integrated transcriptomic and metabolomic analyses revealed the regulatory mechanism of sulfur application in grain yield and protein content in wheat (Triticum aestivum L.)

Sulfur fertilizers play an important role in increasing the yield and improving the dough quality of bread wheat, but their regulatory mechanism remains unclear. In this study, 0 kg·ha^-1 (S0) and 60 kg·ha^-1 (S60) of sulfur were applied on the anthesis date; subsequently, immature wheat grains at 8, 13, and 18 days post-anthesis (DPA) were subjected to integrated transcriptomic and metabolomic analyses to investigate the changes in the gene/metabolite activity in a typical strong-gluten wheat, Gaoyou2018 (GY2018). Our data show that the S60 treatment could significantly increase the grain yield and grain protein content by 13.2 and 3.6%, respectively. The transcriptomic analysis revealed that 10,694 differentially expressed genes (DEGs) were induced by S60 from 8 to 18 DPA when compared with their corresponding no-sulfur controls, and most DEGs were mainly involved in lipid metabolism and amino acid metabolism pathways. Ninety-seven MYB transcription factors (TFs) were identified as responsive to the S60 treatment; of these, 66 showed significantly differential expression at 13 DPA, and MYB118 might participate in the process of sulfur metabolism by regulating glucosinolate synthesis. In total, 542 significantly enriched differentially expressed (DE) metabolites (DEMs) were identified following the S60 treatment, which mainly included secondary metabolites, carbohydrates, and amino acids. Several metabolites (e.g., glutathione, sucrose, GDP-alpha-D-glucose, and amino acids) exhibited altered abundances following the S60 treatment. The combination of transcriptomic and metabolomic analyses highlighted the important role of amino acid metabolism (especially cysteine, methionine, and glutathione metabolism) and starch and sucrose metabolism pathways after S60 application. Our results provide valuable information enhancing our understanding of the molecular mechanism of the response to sulfur and provide useful clues for grain protein quality formation and yield improvement in bread wheat.

Maize kernel development

Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.

Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes

High amylose starch can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava (Manihot esculenta Crantz) with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. All BE1-RNAi plant lines (BE1i) and BE2-RNAi plant lines (BE2i) were grown up in the field, but with reduced total biomass production. Considerably high amylose content in the storage roots of BE2i plant lines was achieved. Storage starch granules of BE1i and BE2i plants had similar morphology as wild type (WT), however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis.

Maize sugary enhancer1 (se1) is a gene affecting endosperm starch metabolism

sugary enhancer1 (se1) is a naturally occurring mutant allele involved in starch metabolism in maize endosperm. It is a recessive modifier of sugary1 (su1) and commercially important in modern sweet corn breeding, but its molecular identity and mode of action remain unknown. Here, we developed a pair of near-isogenic lines, W822Gse (su1-ref/su1-ref se1/se1) and W822GSe (su1-ref/su1-ref Se1/Se1), that Mendelize the se1 phenotype in an su1-ref background. W822Gse kernels have lower starch and higher water soluble polysaccharide and sugars than W822GSe kernels. Using high-resolution genetic mapping, we found that wild-type Se1 is a gene Zm00001d007657 on chromosome 2 and a deletion of this gene causes the se1 phenotype. Comparative metabolic profiling of seed tissue between these 2 isolines revealed the remarkable difference in carbohydrate metabolism, with sucrose and maltose highly accumulated in the mutant. Se1 is predominantly expressed in the endosperm, with low expression in leaf and root tissues. Differential expression analysis identified genes enriched in both starch biosynthesis and degradation processes, indicating a pleiotropic regulatory effect of se1 Repressed expression of Se1 and Su1 in RNA interference-mediated transgenic maize validates that deletion of the gene identified as Se1 is a true causal gene responsible for the se1 phenotype. The findings contribute to our understanding of starch metabolism in cereal crops.

Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents

In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.

The genetic architecture of amylose biosynthesis in maize kernel

Starch is the most abundant storage carbohydrate in maize kernel. The content of amylose and amylopectin confers unique properties in food processing and industrial application. Thus, the resurgent interest has been switched to the study of individual amylose or amylopectin rather than total starch, whereas the enzymatic machinery for amylose synthesis remains elusive. We took advantage of the phenotype of amylose content and the genotype of 9,007,194 single nucleotide polymorphisms from 464 inbred maize lines. The genome-wide association study identified 27 associated loci involving 39 candidate genes that were linked to amylose content including transcription factors, glycosyltransferases, glycosidases, as well as hydrolases. Except the waxy gene that encodes the granule-bound starch synthase, the remaining candidate genes were located in the upstream pathway of amylose synthesis, while the downstream members were already known from prior studies. The linked candidate genes could be transferred to manipulate amylose content and thus add value to maize kernel in the breeding programme.

Sugary Endosperm is Modulated by Starch Branching Enzyme IIa in Rice (Oryza sativa L.)

BACKGROUND

Starch biosynthesis is one of the most important pathways that determine both grain quality and yield in rice (Oryza sativa L.). Sugary endosperm, sugary-1 (sug-1), is a mutant trait for starch biosynthesis. Rice plants carrying sug-1 produce grains that accumulate water-soluble carbohydrates instead of starch, even after maturity. Although this trait enhances the diversity of grain quality, sugary endosperm rice has hardly been commercialized due to the severely wrinkled grains and subsequent problems in milling. This study was conducted to identify the genes responsible for the sug-h phenotype through a map-based cloning technology.

RESULTS

We induced a mild sugary mutant, sugary-h (sug-h) through the chemical mutagenesis on the Korean japonica cultivar Hwacheong. Grains of the sug-h mutant were translucent and amber-colored, and the endosperm appeared less wrinkled than sug-1, whereas the soluble sugar content was fairly high. These characteristics confer greater marketability to the sug-h mutant. Genetic analyses indicated that the sug-h mutant phenotype was controlled by a complementary interaction of two recessive genes, Isoamylase1 (OsISA1), which was reported previously, and Starch branching enzyme IIa (OsBEIIa), which was newly identified in this study. Complementation tests indicated that OsBEIIa regulated the properties of sugary endosperm.

CONCLUSIONS

Complementary interactions between the starch biosynthesis genes OsISA1 and OsBEIIa determine the mild sugary endosperm mutant, sugary-h, in rice. Our finding may facilitate the breeding of sugaryendosperm rice for commercial benefit.

Identification of multiple phosphorylation sites on maize endosperm starch branching enzyme IIb, a key enzyme in amylopectin biosynthesis

Starch branching enzyme IIb (SBEIIb) plays a crucial role in amylopectin biosynthesis in maize endosperm by defining the structural and functional properties of storage starch and is regulated by protein phosphorylation. Native and recombinant maize SBEIIb were used as substrates for amyloplast protein kinases to identify phosphorylation sites on the protein. A multidisciplinary approach involving bioinformatics, site-directed mutagenesis, and mass spectrometry identified three phosphorylation sites at Ser residues: Ser(649), Ser(286), and Ser(297). Two Ca(2+)-dependent protein kinase activities were partially purified from amyloplasts, termed K1, responsible for Ser(649) and Ser(286) phosphorylation, and K2, responsible for Ser(649) and Ser(297) phosphorylation. The Ser(286) and Ser(297) phosphorylation sites are conserved in all plant branching enzymes and are located at opposite openings of the 8-stranded parallel β-barrel of the active site, which is involved with substrate binding and catalysis. Molecular dynamics simulation analysis indicates that phospho-Ser(297) forms a stable salt bridge with Arg(665), part of a conserved Cys-containing domain in plant branching enzymes. Ser(649) conservation appears confined to the enzyme in cereals and is not universal, and is presumably associated with functions specific to seed storage. The implications of SBEIIb phosphorylation are considered in terms of the role of the enzyme and the importance of starch biosynthesis for yield and biotechnological application.

RETRACTED: Molecular strategies in manipulation of the starch synthesis pathway for improving storage starch content in plants (review and prospect for increasing storage starch synthesis)

Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bioethanol production. In recent decades, enormous progress has been made in understanding the genetic and biochemical mechanisms of starch synthesis in plants. Yet, despite this remarkable progress and its obvious economic importance, very little has been achieved in terms of adding value to starch or increasing starch content, particularly in cereal crops. In this paper, we first review recent advances in understanding the biochemistry of starch synthesis, particularly in identifying key enzymes involved in starch assembly. We then assess the progress in molecular strategies for improving storage starch content in plants. Finally, we discuss the problems faced in our profession and present ideas to effectively increase storage starch content in the future.

Biomolecular analyses of starch and starch granule proteins in the high-amylose rice mutant Goami 2

Elevated proportions of amylose in cereals are commonly associated with either the loss of starch branching or starch synthase activity. Goami 2 is a high-amylose mutant of the temperate japonica rice variety Ilpumbyeo. Genotyping revealed that Goami 2 and Ilpumbyeo carry the same alleles for starch synthase IIa and granule-bound starch synthase I genes. Analyses of granule-bound proteins revealed that SSI and SSIIa accumulate inside the mature starch granules of Goami 2, which is similar to the amylose extender mutant IR36ae. However, unlike the amylose extender mutants, SBEIIb was still detectable inside the starch granules of Goami 2. Detection of SBEIIb after protein fractionation revealed that most of the SBEIIb in Goami 2 accumulates inside the starch granules, whereas most of it accumulates at the granule surface in Ilpumbyeo. Exhaustive mass spectrometric characterisations of granule-bound proteins failed to detect any peptide sequence mutation or major post-translational modifications in Goami 2. Moreover, the signal peptide was found to be cleaved normally from the precursor protein, and there is no apparent N-linked glycosylation. Finally, no difference was found in the SBEIIb structural gene sequence of Goami 2 compared with Ilpumbyeo. In contrast, a G-to-A mutation was detected in the SBEIIb gene of IR36ae located at the splice site between exon and intron 11, which could potentially introduce a premature stop codon and produce a truncated form of SBEIIb. It is suggested that the mutation responsible for producing high amylose in Goami 2 is not due to a defect in SBEIIb gene as was observed in IR36ae, even though it produces a phenotype analogous to the amylose extender mutation. Understanding the molecular genetic basis of this mutation will be important in identifying novel targets for increasing amylose and resistant starch contents in rice and other cereals.

Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing

The inactivation of starch branching IIb (SBEIIb) in rice is traditionally associated with elevated apparent amylose content, increased peak gelatinization temperature, and a decreased proportion of short amylopectin branches. To elucidate further the structural and functional role of this enzyme, the phenotypic effects of down-regulating SBEIIb expression in rice endosperm were characterized by artificial microRNA (amiRNA) and hairpin RNA (hp-RNA) gene silencing. The results showed that RNA silencing of SBEIIb expression in rice grains did not affect the expression of other major isoforms of starch branching enzymes or starch synthases. Structural analyses of debranched starch showed that the doubling of apparent amylose content was not due to an increase in the relative proportion of amylose chains but instead was due to significantly elevated levels of long amylopectin and intermediate chains. Rices altered by the amiRNA technique produced a more extreme starch phenotype than those modified using the hp-RNA technique, with a greater increase in the proportion of long amylopectin and intermediate chains. The more pronounced starch structural modifications produced in the amiRNA lines led to more severe alterations in starch granule morphology and crystallinity as well as digestibility of freshly cooked grains. The potential role of attenuating SBEIIb expression in generating starch with elevated levels of resistant starch and lower glycaemic index is discussed.

Starch accumulation, activities of key enzyme and gene expression in starch synthesis of wheat endosperm with different starch contents

In order to investigate starch accumulation, and the enzymes activity changes and the expression levels of genes and their relationships among them at different developmental stages of wheat grain. We choose Annong9912 and E28 were used in the study. During starch accumulating rate and grain filling rate, and there were obvious genotype difference between Annong9912 and E28. Whether low or high starch content of starch content, the accumulation courses of amylopectin, amylose and total starch were well fitted to the logistic equation by relating starch contents against DAP. The simulation parameters revealed that the higher contents of amylopectin and amylose resulted from earlier initiating accumulation time and greater accumulation rate. And amylose, amylopectin and total starch accumulation rate of two wheat cultures were significantly and positively correlated with activities of SBE, SSS and GBSS, but amylose accumulation rate of E28 had no correlation with the activities of SBE. In addition, there were significant correlations among activities of SBE, SSS and GBSS in two wheat cultivars. We speculated that these enzymes proteins may have a coordinating action in starch biosynthesis within the amyloplast, operating as functional multiprotein complexes. And expression levels of enzyme genes demonstrated a single-peak curve, and 12-18 DAP reached their peaks and then began to drop, and all had high expression level in earlier stage of endosperm development, but in E28 were higher than in Annong9912. The GBSS-I transcripts on average were expressed over 60 times more than GBSS-II transcript in E28. SBE, SSS, DBE may control starch synthesis at the transcriptional level, and GBSS-I may control starch synthesis at the post transcriptional level. The expression level of DBE on average was lower than SS-1 and SBE-IIa genes, and similar to SS-III and SBE-IIb genes, but higher than GBSS-I and GBSS-II genes.

Deficiency of maize starch-branching enzyme I results in altered starch fine structure, decreased digestibility and reduced coleoptile growth during germination

BACKGROUND

Two distinct starch branching enzyme (SBE) isoforms predate the divergence of monocots and dicots and have been conserved in plants since then. This strongly suggests that both SBEI and SBEII provide unique selective advantages to plants. However, no phenotype for the SBEI mutation, sbe1a, had been previously observed. To explore this incongruity the objective of the present work was to characterize functional and molecular phenotypes of both sbe1a and wild-type (Wt) in the W64A maize inbred line.

RESULTS

Endosperm starch granules from the sbe1a mutant were more resistant to digestion by pancreatic α-amylase, and the sbe1a mutant starch had an altered branching pattern for amylopectin and amylose. When kernels were germinated, the sbe1a mutant was associated with shorter coleoptile length and higher residual starch content, suggesting that less efficient starch utilization may have impaired growth during germination.

CONCLUSIONS

The present report documents for the first time a molecular phenotype due to the absence of SBEI, and suggests strongly that it is associated with altered physiological function of the starch in vivo. We believe that these results provide a plausible rationale for the conservation of SBEI in plants in both monocots and dicots, as greater seedling vigor would provide an important survival advantage when resources are limited.

Synergistic influence of sucrose and abscisic acid on the genes involved in starch synthesis in maize endosperm

Starch is the major carbon reserve in plant storage organs, the synthesis of which is orchestrated by four major enzymes, ADP-glucose pyrophosphorylase, starch synthase, starch-branching enzyme and starch-debranching enzyme. There is much information available on the function of these key enzymes; however, little is known about their transcriptional regulation. In order to understand the transcriptional regulation of starch biosynthesis, the expression profiles of 24 starch genes were investigated in this work. The results showed major transcriptional changes for 15 of the 24 starch genes observed in maize endosperm, most of which are elevated at the early and middle stages of the developing endosperm. Sucrose, abscisic acid (ABA) and indole-3-acetic acid (IAA) had a significant correlation with the expression of 15 genes, indicating that sugars and phytohormones might take part in the regulation of starch synthesis. Also, we found that there is interaction of abscisic acid and sucrose on the regulation of the expression of these genes.

Molecular marker-assisted selection of the ae alleles in maize

The ae (amylose extender) recessive mutant alleles in maize are an important genetic resource for the development of high-amylose cultivars. On the basis of ae allele sequences (from the National Center for Biotechnology Information), the ae mutant alleles were cloned from high-amylose maize and the allelic Ae gene from common maize luyuan92 inbred lines. Five pairs of primers were designed to screen for a molecular marker of ae alleles, yielding a dominant molecular marker, ae474. We used 53 types of high-amylose maize and common maize inbred lines and their hybrid and backcross offspring for verification and analysis. The ae dominant molecular marker was effective in selecting for the ae alleles and for biological materials with a high-amylose genotype. Presence and absence of the marker in the offspring conformed to the expected Mendelian ratios. Using this marker, we were able to detect the ae alleles in a backcross and its second generation more efficiently (53.3 and 73.3%, respectively) than was possible without marker selection. These data indicate that the marker can be used as a tool to improve selection efficiency and accelerate the cultivation of new varieties of high-amylose maize.

Diurnal oscillation of SBE expression in sorghum endosperm

Spatial and temporal expression patterns of the sorghum SBEI, SBEIIA and SBEIIB genes, encoding, respectively, starch branching enzyme (SBE) I, IIA and IIB, in the developing endosperm of sorghum (Sorghum bicolor) were studied. Full-length genomic and cDNA clones for sorghum were cloned, and the SBEIIA cDNA was used together with gene-specific probes for sorghum SBEIIB and SBEI. In contrast to sorghum SBEIIB, which was expressed primarily in endosperm and embryo, SBEIIA was also expressed in vegetative tissues. All three genes shared a similar temporal expression profile during endosperm development, with a maximum activity at 15-24 d after pollination. This differed from barley and maize, in which SBEI gene activity showed a significantly later onset compared to that of SBEIIA and SBEIIB. Expression of the three SBE genes in the sorghum endosperm exhibited a diurnal rhythm during a 24-h cycle.

Nutritional property of endosperm starches from maize mutants: a parabolic relationship between slowly digestible starch and amylopectin fine structure

The relationship between the slow digestion property of cooked maize starch and its molecular fine structure was investigated. Results of the in vitro Englyst assay showed a range of rapidly digestible starch (RDS) (70.1-98.9%), slowly digestible starch (SDS) (0.2-20.3%), and resistant starch (RS) (0.0-13.7%) among the tested maize mutant flour samples. Further analysis showed that amylose content was significantly correlated ( R = 0.763, P < 0.001) with RS amount but not with that of SDS, indicating that amylopectin is the starch molecule associated with SDS. Total starch debranching analysis revealed a parabolic relationship between SDS content and the weight ratio of amylopectin short chains (DP < 13, named SF) to long chains (DP >/= 13, named LF), which means amylopectin with a higher amount of either short chains or long chains can produce relatively high amounts of SDS. Furthermore, debranching analysis of the SDS materials from samples with the highest and lowest weight ratios of SF/LF (both had a high amount SDS) showed significantly different profiles, indicating there is not a uniform molecular structure for SDS. Thus, genetic mutants of maize samples have a good potential to provide raw starch materials of high nutritional quality. An additional finding showed that a simple and comparably high-throughput technique of Rapid Visco-Analyzer (RVA) can be used to screen genetic mutants on the basis of their RVA profiles.

Mutation of the maize sbe1a and ae genes alters morphology and physical behavior of wx-type endosperm starch granules

In maize, three isoforms of starch-branching enzyme, SBEI, SBEIIa, and SBEIIb, are encoded by the Sbe1a, Sbe2a, and Amylose extender (Ae) genes, respectively. The objective of this research was to explore the effects of null mutations in the Sbe1a and Ae genes alone and in combination in wx background on kernel characteristics and on the morphology and physical behavior of endosperm starch granules. Differences in kernel morphology and weight, starch accumulation, starch granule size and size distribution, starch microstructure, and thermal properties were observed between the ae wx and sbe1a ae wx plants but not between the sbe1a wx mutants when compared to wx. Starch from sbe1a ae wx plants exhibited a larger granule size with a wider gelatinization temperature range and a lower endotherm enthalpy than ae wx. Microscopy shows weaker iodine staining in sbe1a ae wx starch granules. X-ray diffraction revealed A-type crystallinity in wx and sbe1a wx starches and B-type in sbe1a ae wx and ae wx. This study suggests that, while the SBEIIb isoform plays a dominant role in maize endosperm starch synthesis, SBEI also plays a role, which is only observable in the presence of the ae mutation.

Genomic isolation of genes encoding starch branching enzyme II (SBEII) in apple: toward characterization of evolutionary disparity in SbeII genes between monocots and eudicots

Two genes encoding starch branching enzyme II (SBEII) have been identified in apple. These genes share 94 and 92% identity in coding DNA sequences and amino acid sequences, respectively; moreover, they have similar expression patterns. Both genes are expressed in vegetative and reproductive tissues, including leaves, buds, flowers, and fruits. Based on genomic Southern blots, there are two copies of SbeII genes in the apple genome. Comparisons of genomic sequences between monocots and eudicots have revealed that the genomic structure of SbeII genes is conserved. However, the 5'-terminal region of coding DNA sequences of SbeII genes shows greater divergence than the 3'-terminal region between monocots and eudicots. Phylogenetic analysis of DNA sequences has demonstrated that the duplication patterns of SbeII genes are different between monocots and eudicots. In monocots, the duplication of SbeII genes must have occurred prior to the radiation of grasses (Poaceae); while, in eudicots, the expansion of SbeII genes must have followed the process of speciation.

Three orthologs in rice, Arabidopsis, and Populus encoding starch branching enzymes (SBEs) are different from other SBE gene families in plants

Starch branching enzymes (SBEs) play important roles in plant starch synthesis. Three orthologs encoding SBEs in rice, Arabidopsis thaliana, and Populus trichocarpa are described. Putative amino acid sequences of these three SBE genes show approximately 30% identity to those of SBEI and SBEII from plants such as maize, barley, and wheat. More interestingly, they share approximately 31% amino acid sequence identity with those of glycogen-branching enzymes from such animals as mouse, horse, and monkey. The three genes have similar genomic structures, but their structural features are quite different from those of genes of both SBEI and SBEII families in plants. Based on phylogenetic analysis and genomic structure comparison, it is proposed that the three SBE genes represent a new family of SBEs.

A gene encoding starch branching enzyme I (SBEI) in apple (Malusxdomestica, Rosaceae) and its phylogenetic relationship to Sbe genes from other angiosperms

An apple starch-branching enzyme SbeI gene (GenBank Accession No. DQ115404) has been isolated, cloned, and sequenced. The SbeI is a single copy gene in the apple genome, consisting of 14 exons and 13 introns, and covering 6075bp. As detected by RT-PCR, the apple SbeI is expressed at very low levels during early stages of fruit development; while, the highest levels of mRNA transcripts are observed at approximately 44 days post-pollination. Besides fruits, the apple SbeI is also expressed in buds and flowers, and very weakly in leaves. The genomic structure of SbeI in apple is strikingly similar to those reported so far in grasses (Poaceae), with exons 4 through 13 being of identical lengths in both apple and grasses. Moreover, structure similarities in exon lengths have also been detected in SbeII genes of both grasses and eudicots. These findings prompted the investigation of the evolutionary process of the Sbe gene family in angiosperms. A total of 26 Sbe sequences, representing an array of monocots and eudicots, are investigated in this study. Phylogenetic analysis has suggested that Sbe genes have duplicated into SbeI and SbeII prior to the divergence of moncots from eudicots. The SbeII gene is further duplicated into SbeIIa and SbeIIb prior to the radiation of grasses; however, it is not yet clear whether this duplication event has occurred before or after the radiation of the eudicots.

Starch branching enzyme IIb in wheat is expressed at low levels in the endosperm compared to other cereals and encoded at a non-syntenic locus

Studies of maize starch branching enzyme mutants suggest that the amylose extender high amylose starch phenotype is a consequence of the lack of expression of the predominant starch branching enzyme II isoform expressed in the endosperm, SBEIIb. However, in wheat, the ratio of SBEIIb and SBEIIa expression are inversely related to the expression levels observed in maize and rice. Analysis of RNA at 15 days post anthesis suggests that there are about 4-fold more RNA for SBE IIa than for SBE IIb. The genes for SBE IIa and SBE IIb from wheat are distinguished in the size of the first three exons, allowing isoform-specific antibodies to be produced. These antibodies were used to demonstrate that in the soluble fraction, the amount of SBE IIa protein is two to three fold higher than SBIIb, whereas in the starch granule, there is two to three fold more SBE IIb protein amount than SBE IIa. In a further difference to maize and rice, the genes for SBE IIa and SBE IIb are both located on the long arm of chromosome 2 in wheat, in a position not expected from rice-maize-wheat synteny.

Starch branching enzymes in sorghum (Sorghum bicolor) and barley (Hordeum vulgare): comparative analyses of enzyme structure and gene expression

A genomic clone for starch branching enzyme (SBE) IIb was isolated from a sorghum bacterial artificial chromosome (BAC) library. The promoter and 5' flanking sequence, the first four exons and introns as well as the last exon and the 3' untranslated region were sequenced. The tentative transcription start site of sorghum sbeIIb was mapped based on alignment with the maize sbeIIb gene. The exon-intron structure of the 5' portion of sorghum sbeIIb was similar to that of maize sbeIIb but differed from that of barley sbeIIb. Specifically, the intronic BbI element involved in the endosperm specific expression of barley sbeIIb was lacking in the sorghum gene. A cDNA clone for sorghum sbeIIb was reverse PCR amplified and found to encode an 803 amino acids long protein. The amino acid sequence of sorghum SBEIIb was compared to that of sorghum SBEI and corresponding enzymes in barley. The overall identity in amino acid sequence was 54% in the central portion of the enzymes. A major difference between the SBEII and SBEI isoforms was a 67 amino acids-long C-terminal extension in the SBEIs. The spatial and temporal expression patterns of sorghum sbeIIb was determined and compared with those of the sorghum gene for SBEI and the barley genes for SBEIIB and SBEI. All four genes exhibited a seed specific expression. However, while barley sbeIIb and sbeI transcripts were detected exclusively in the endosperm, the sorghum genes were expressed also in the embryo. The activity of sorghum sbeIIb and sbeI exhibited a late onset, with a peak of transcription at around 22 days after pollination. This is similar to the pattern of barley sbeI but different from that of barley sbeIIb, which showed a peak of transcription at 12 days after pollination.

Characterization of a gene from chromosome 1B encoding the large subunit of ADPglucose pyrophosphorylase from wheat: evolutionary divergence and differential expression of Agp2 genes between leaves and developing endosperm

A full-length genomic clone containing the gene encoding the large subunit of the ADPglucose pyrophosphorylase (Agp2), was isolated from a genomic library prepared from etiolated shoots of hexaploid wheat (Triticum aestivum L., cv, Chinese Spring). The coding region of this gene is identical to one of the cDNA clones previously isolated from a developing wheat grain cDNA library and is therefore an actively transcribed gene. The sequence represented by the cDNA spans 4.8 kb of the genomic clone and contains 15 introns. 2852 bp of DNA flanking the transcription start site of the gene was cloned upstream of the GUS (beta-glucuronidase) reporter gene. This Agp2::GUS construct and promoter deletions were used to study the pattern of reporter gene expression in both transgenic tobacco and wheat plants. Histochemical analysis of GUS expression in transgenic tobacco demonstrated that the reporter gene was expressed in guard cells of leaves and throughout the seed. In transgenic wheat, reporter gene expression was confined to the endosperm and aleurone with no expression in leaves. The cloned Agp2 gene was located to chromosome 1B by gene-specific PCR with nullisomic-tetrasomic lines. Northern analysis demonstrated that the Agp2 genes are differentially expressed in leaves and developing endosperm; while all three classes of Agp2 genes are transcribed in developing wheat grain endosperm, only one is transcribed in leaves. The differences between the Agp2 genes are discussed in relation to the evolution of hexaploid wheat.

Role of granule-bound starch synthase in determination of amylopectin structure and starch granule morphology in potato

Reductions in activity of SSIII, the major isoform of starch synthase responsible for amylopectin synthesis in the potato tuber, result in fissuring of the starch granules. To discover the causes of the fissuring, and thus to shed light on factors that influence starch granule morphology in general, SSIII antisense lines were compared with lines with reductions in the major granule-bound isoform of starch synthase (GBSS) and lines with reductions in activity of both SSIII and GBSS (SSIII/GBSS antisense lines). This revealed that fissuring resulted from the activity of GBSS in the SSIII antisense background. Control (untransformed) lines and GBSS and SSIII/GBSS antisense lines had unfissured granules. Starch analyses showed that granules from SSIII antisense tubers had a greater number of long glucan chains than did granules from the other lines, in the form of larger amylose molecules and a unique fraction of very long amylopectin chains. These are likely to result from increased flux through GBSS in SSIII antisense tubers, in response to the elevated content of ADP-glucose in these tubers. It is proposed that the long glucan chains disrupt organization of the semi-crystalline parts of the matrix, setting up stresses in the matrix that lead to fissuring.

Two starch-branching-enzyme isoforms occur in different fractions of developing seeds of kidney bean

The nature and enzymic properties of starch-branching enzyme (SBE) are two of the dominant factors influencing the fine structure of starch. To understand the role of this enzyme's activity in the formation of starch in kidney bean (Phaseolus vulgaris L.), a study was undertaken to identify the major SBE sequences expressed during seed development and to characterize the enzymic properties of the coded recombinant enzymes. Two SBE cDNA species (designated pvsbe2 and pvsbe1) that displayed significant similarity (more than 70%) to other family A and B SBEs respectively were isolated. Northern blot analysis revealed that pvsbe1 and pvsbe2 were differentially expressed during seed development. pvsbe2 showed maximum steady-state transcript levels at the mid-stage of seed maturation, whereas pvsbe1 reached peak levels at a later stage. Western blot analysis with antisera raised against both recombinant proteins (rPvSBE1 and rPvSBE2) showed that these two SBEs were located in different amyloplast fractions of developing seeds of kidney bean. PvSBE2 was present in the soluble fraction, whereas PvSBE1 was associated with the starch granule fraction. The differences in location suggest that these two SBE isoenzymes have different roles in amylopectin synthesis in kidney bean seeds. rPvSBE1 and rPvSBE2 were purified from Escherichia coli and their kinetic properties were determined. The affinity of rPvSBE2 for amylose (K(m) 1.27 mg/ml) was lower than that of rPvSBE1 (0.46 mg/ml). The activity of rPvSBE2 was stimulated more than 3-fold in the presence of 0.3 M citrate, whereas rPvSBE1 activity was not affected. The implications of the enzymic properties and the distribution of SBEs and amylopectin structure are discussed.

Comparison of starch-branching enzyme genes reveals evolutionary relationships among isoforms. Characterization of a gene for starch-branching enzyme IIa from the wheat genome donor Aegilops tauschii

Genes and cDNAs for starch-branching enzyme II (SBEII) have been isolated from libraries constructed from Aegilops tauschii and wheat (Triticum aestivum) endosperm, respectively. One class of genes has been termed wSBEII-DA1 and encodes the N terminus reported for an SBEII from wheat endosperm. On the basis of phylogenetic comparisons with other branching enzyme sequences, wSBEII-DA1 is considered to be a member of the SBEIIa class. The wSBEII-DA1 gene consists of 22 exons with exons 4 to 21 being identical in length to the maize (Zea mays) SBEIIb gene, and the gene is located in the proximal region of the long arm of chromosome 2 at a locus designated sbe2a. RNA encoding SBEIIa can be detected in the endosperm from 6 d after flowering and is at its maximum level from 15 to 18 d after anthesis. Use of antibodies specific for SBEIIa demonstrated that this protein was present in both the soluble and granule bound fractions in developing wheat endosperm. We also report a cDNA sequence for SBEIIa that could arise by variant transcription/splicing. A second gene, termed wSBEII-DB1, was isolated and encodes an SBEII, which shows greater sequence identity with SBEIIb-type sequences than with SBEIIa-type sequences. Comparisons of SBEII gene structures among wheat, maize, and Arabidopsis indicate the lineage of the SBEII genes.

Identification of Mutator insertional mutants of starch-branching enzyme 2a in corn

Starch-branching enzymes (SBE) break the alpha-1,4 linkage of starch, re-attaching the chain to a glucan chain by an alpha-1,6 bond, altering starch structure. SBEs also facilitate starch accumulation by increasing the number of non-reducing ends on the growing chain. In maize (Zea mays), three isoforms of SBE have been identified. To examine the function of the SBEIIa isoform, a reverse genetics polymerase chain reaction-based screen was used to identify a mutant line segregating for a Mutator transposon within Sbe2a. To locate the insertion within the second exon of Sbe2a, the genomic sequence of Sbe2a containing the promoter and 5' end was isolated and sequenced. Plants homozygous for sbe2a::Mu have undetectable levels of Sbe2a transcripts and SBEIIa in their leaves. Characterization of leaf starch from sbe2a::Mu mutants shows reduced branching similar to yet more extreme than that seen in kernels lacking SBEIIb activity. Characterization of endosperm starch from sbe2a::Mu mutants shows branching that is indistinguishable from wild-type controls. These mutant plants have a visible phenotype resembling accelerated senescence, which was correlated with the Mutator insertion within Sbe2a. This correlation suggests a specific role for SBEIIa in leaves, which may be necessary for normal plant development.

A maize sesquiterpene cyclase gene induced by insect herbivory and volicitin: characterization of wild-type and mutant alleles

Plants can defend themselves from herbivorous insects by emitting volatile chemical signals that attract natural enemies of the herbivore. For example, maize seedlings attacked by beet armyworm larvae (Spodoptera exigua) produce a mixture of terpenoid and indole volatiles that serve to attract parasitic wasps. A key step in terpenoid biosynthesis is the conversion of acyclic prenyl diphosphates to terpenoid compounds by specific terpenoid synthases (cyclases). We have cloned a maize sesquiterpene cyclase gene, stc1, by transposon tagging and have identified two deletion mutations of the gene. The stc1 gene is located on chromosome 9S and does not seem to have a closely related ortholog in the maize genome. It is induced 15- to 30-fold in maize leaves by beet armyworm larvae feeding or by application of purified volicitin, the insect-derived elicitor, at a mechanically wounded site. stc1 induction is systemic, because undamaged leaves of the same plant show a similar increase in stc1 transcription. Analysis of volatiles from volicitin-treated seedlings revealed that a major naphthalene-based sesquiterpene was present in wild-type seedlings but absent in the Ac-insertion and x-ray-deletion mutants. Therefore, we have identified a maize gene that responds to caterpillar herbivory by producing a chemical defense signal that most likely serves to attract natural enemies of the herbivore.

Identification of cis-acting elements important for expression of the starch-branching enzyme I gene in maize endosperm

The genes encoding the starch-branching enzymes (SBE) SBEI, SBEIIa, and SBEIIb in maize (Zea mays) are differentially regulated in tissue specificity and during kernel development. To gain insight into the regulatory mechanisms controlling their expression, we analyzed the 5'-flanking sequences of Sbe1 using a transient gene expression system. Although the 2.2-kb 5'-flanking sequence between -2,190 and +27 relative to the transcription initiation site was sufficient to promote transcription, the addition of the transcribed region between +28 and +228 containing the first exon and intron resulted in high-level expression in suspension-cultured maize endosperm cells. A series of 5' deletion and linker-substitution mutants identified two critical positive cis elements, -314 to -295 and -284 to -255. An electrophoretic mobility-shift assay showed that nuclear proteins prepared from maize kernels interact with the 60-bp fragment containing these two elements. Expression of the Sbe1 gene is regulated by sugar concentration in suspension-cultured maize endosperm cells, and the region -314 to -145 is essential for this effect. Interestingly, the expression of mEmBP-1, a bZIP transcription activator, in suspension-cultured maize endosperm cells resulted in a 5-fold decrease in Sbe1 promoter activity, suggesting a possible regulatory role of the G-box present in the Sbe1 promoter from -227 to -220.