Immunological characterization of maize starch branching enzymes

Trihelix Transcription Factor ZmThx20 Is Required for Kernel Development in Maize

Maize kernels are the harvested portion of the plant and are related to the yield and quality of maize. The endosperm of maize is a large storage organ that constitutes 80–90% of the dry weight of mature kernels. Maize kernels have long been the study of cereal grain development to increase yield. In this study, a natural mutation that causes abnormal kernel development, and displays a shrunken kernel phenotype, was identified and named “shrunken 2008 (sh2008)”. The starch grains in sh2008 are loose and have a less proteinaceous matrix surrounding them. The total storage protein and the major storage protein zeins are ~70% of that in the wild-type control (WT); in particular, the 19 kDa and 22 kDa α-zeins. Map-based cloning revealed that sh2008 encodes a GT-2 trihelix transcription factor, ZmThx20. Using CRISPR/Cas9, two other alleles with mutated ZmThx20 were found to have the same abnormal kernel. Shrunken kernels can be rescued by overexpressing normal ZmThx20. Comparative transcriptome analysis of the kernels from sh2008 and WT showed that the GO terms of translation, ribosome, and nutrient reservoir activity were enriched in the down-regulated genes (sh2008/WT). In short, these changes can lead to defects in endosperm development and storage reserve filling in seeds.

Microsatellite-based genetic diversity analyses of sugary1-, shrunken2- and double mutant- sweet corn inbreds for their utilization in breeding programme

Sweet corn has recently experienced sharp rise in demand worldwide. Recessive sugary1 (su1) and shrunken2 (sh2) that enhances kernel sweetness have been abundantly used in sweet corn breeding. Analyses of genetic diversity among sweet corn inbreds assume great significance for their effective utilization in hybrid breeding. A set of 48 diverse sweet corn genotypes encompassing su1su1, sh2sh2 and su1su1/sh2sh2 types were analyzed using 56 microsatellite markers. A total of 213 alleles with mean of 3.8 alleles per locus were generated. Two unique- and 12 rare- alleles were identified. The average PIC and genetic dissimilarity was 0.50 and 0.73, respectively. Cluster analysis grouped the inbreds into three major clusters, with each of the su1su1-, sh2sh2- and su1su1/sh2sh2-types were broadly clustered together. Principal coordinate analyses also depicted the diverse origin of the genotypes. The study identified inbreds for synthesis of pools and pedigree populations to develop novel inbreds. The study led to the identification of prospective heterotic combinations in various genetic backgrounds (sh2sh2 × sh2sh2, su1su1 × su1su1, su1su1/sh2sh2 × su1su1/sh2sh2, sh2sh2 × su1su1/sh2sh2 and su1su1 × su1su1/sh2sh2).

Genetic diversity of maize kernel starch-synthesis genes with SNAPs

Measuring genetic diversity in populations of a crop species is very important for understanding the genetic structure of and subsequently improving the crop species by genetic manipulation. Single-nucleotide amplified polymorphisms (SNAPs) among and within maize populations of waxy, dent, and sweet corns at 25 single-nucleotide polymorphism (SNP) sites in 6 kernel starch-synthesis genes (sh2, bt2, su1, ae1, wx1, and sh1) were determined. Because of the intensive selection of some favorable alleles in starch-synthesis genes during the breeding process, and the resultant strong linkage disequilibrium (LD), the number of haplotypes in each population was far less than expected. Subsequent phenetic clustering analysis with the SNAPs indicated that the dent, waxy, and sweet corns formed distinct subclusters, except in a few incidences. LD was surveyed among SNAPs of intragenic, intergenic, and intrachromosomal SNPs in whole and subpopulations, which revealed that some SNAPs showed high LD with many other SNAPs, but some SNAPs showed low or no significant LD with others, depending on the subpopulation, indicating that these starch genes have undergone different selection in each subpopulation during the breeding process. Because the starch synthesis genes used in this study are important in maize breeding, the genetic diversity, LD, and accessions having rare SNAP alleles might be valuable in maize improvement programs.

Starch-branching enzyme I-deficient mutation specifically affects the structure and properties of starch in rice endosperm

We have isolated a starch mutant that was deficient in starch-branching enzyme I (BEI) from the endosperm mutant stocks of rice (Oryza sativa) induced by the treatment of fertilized egg cells with N-methyl-N-nitrosourea. The deficiency of BEI in this mutant was controlled by a single recessive gene, tentatively designated as starch-branching enzyme mutant 1 (sbe1). The mutant endosperm exhibited the normal phenotype and contained the same amount of starch as the wild type. However, the mutation apparently altered the fine structure of amylopectin. The mutant amylopectin was characterized by significant decrease in both long chains with degree of polymerization (DP) > or = 37 and short chains with DP 12 to 21, marked increase in short chains with DP < or = 10 (A chains), and slight increase in intermediate chains with DP 24 to 34, suggesting that BEI specifically synthesizes B1 and B2-3 chains. The endosperm starch from the sbe1 mutant had a lower onset concentration for urea gelatinization and a lower onset temperature for thermo-gelatinization compared with the wild type, indicating that the genetic modification of amylopectin fine structure is responsible for changes in physicochemical properties of sbe1 starch.

Genetic diversity and selection in the maize starch pathway

Maize is both phenotypically and genetically diverse. Sequence studies generally confirm the extensive genetic variability in modern maize is consistent with a lack of selection. For more than 6,000 years, Native Americans and modern breeders have exploited the tremendous genetic diversity of maize (Zea mays ssp. mays) to create the highest yielding grain crop in the world. Nonetheless, some loci have relatively low levels of genetic variation, particularly loci that have been the target of artificial selection, like c1 and tb1. However, there is limited information on how selection may affect an agronomically important pathway for any crop. These pathways may retain the signature of artificial selection and may lack genetic variation in contrast to the rest of the genome. To evaluate the impact of selection across an agronomically important pathway, we surveyed nucleotide diversity at six major genes involved in starch metabolism and found unusually low genetic diversity and strong evidence of selection. Low diversity in these critical genes suggests that a paradigm shift may be required for future maize breeding. Rather than relying solely on the diversity within maize or on transgenics, future maize breeding would perhaps benefit from the incorporation of alleles from maize's wild relatives.

Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm

Biochemical analysis of amylose-extender (ae) mutant of rice (Oryza sativa) revealed that the mutation in the gene for starch-branching enzyme IIb (BEIIb) specifically altered the structure of amylopectin in the endosperm by reducing short chains with degree of polymerization of 17 or less, with the greatest decrease in chains with degree of polymerization of 8 to 12. The extent of such change was correlated with the gelatinization properties of the starch granules, as determined in terms of solubility in urea solution. The ae mutation caused a dramatic reduction in the activity of BEIIb. The activity of soluble starch synthase I (SSI) in the ae mutant was significantly lower than in the wild type, suggesting that the mutation had a pleiotropic effect on the SSI activity. In contrast, the activities of BEI, BEIIa, ADP-Glc pyrophosphorylase, isoamylase, isoamylase, pullulanase, and Suc synthase were not affected by the mutation. Therefore, it is stressed that the function of BEIIb cannot be complemented by BEIIa and BEI. These results strongly suggest that BEIIb plays a specific role in the transfer of short chains, which might then be extended by SS to form the A and B(1) chains of amylopectin cluster in rice endosperm.

Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm

Biochemical analysis of amylose-extender (ae) mutant of rice (Oryza sativa) revealed that the mutation in the gene for starch-branching enzyme IIb (BEIIb) specifically altered the structure of amylopectin in the endosperm by reducing short chains with degree of polymerization of 17 or less, with the greatest decrease in chains with degree of polymerization of 8 to 12. The extent of such change was correlated with the gelatinization properties of the starch granules, as determined in terms of solubility in urea solution. The ae mutation caused a dramatic reduction in the activity of BEIIb. The activity of soluble starch synthase I (SSI) in the ae mutant was significantly lower than in the wild type, suggesting that the mutation had a pleiotropic effect on the SSI activity. In contrast, the activities of BEI, BEIIa, ADP-Glc pyrophosphorylase, isoamylase, isoamylase, pullulanase, and Suc synthase were not affected by the mutation. Therefore, it is stressed that the function of BEIIb cannot be complemented by BEIIa and BEI. These results strongly suggest that BEIIb plays a specific role in the transfer of short chains, which might then be extended by SS to form the A and B(1) chains of amylopectin cluster in rice endosperm.

Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm

Biochemical analysis of amylose-extender (ae) mutant of rice (Oryza sativa) revealed that the mutation in the gene for starch-branching enzyme IIb (BEIIb) specifically altered the structure of amylopectin in the endosperm by reducing short chains with degree of polymerization of 17 or less, with the greatest decrease in chains with degree of polymerization of 8 to 12. The extent of such change was correlated with the gelatinization properties of the starch granules, as determined in terms of solubility in urea solution. The ae mutation caused a dramatic reduction in the activity of BEIIb. The activity of soluble starch synthase I (SSI) in the ae mutant was significantly lower than in the wild type, suggesting that the mutation had a pleiotropic effect on the SSI activity. In contrast, the activities of BEI, BEIIa, ADP-Glc pyrophosphorylase, isoamylase, isoamylase, pullulanase, and Suc synthase were not affected by the mutation. Therefore, it is stressed that the function of BEIIb cannot be complemented by BEIIa and BEI. These results strongly suggest that BEIIb plays a specific role in the transfer of short chains, which might then be extended by SS to form the A and B(1) chains of amylopectin cluster in rice endosperm.

Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm

Biochemical analysis of amylose-extender (ae) mutant of rice (Oryza sativa) revealed that the mutation in the gene for starch-branching enzyme IIb (BEIIb) specifically altered the structure of amylopectin in the endosperm by reducing short chains with degree of polymerization of 17 or less, with the greatest decrease in chains with degree of polymerization of 8 to 12. The extent of such change was correlated with the gelatinization properties of the starch granules, as determined in terms of solubility in urea solution. The ae mutation caused a dramatic reduction in the activity of BEIIb. The activity of soluble starch synthase I (SSI) in the ae mutant was significantly lower than in the wild type, suggesting that the mutation had a pleiotropic effect on the SSI activity. In contrast, the activities of BEI, BEIIa, ADP-Glc pyrophosphorylase, isoamylase, isoamylase, pullulanase, and Suc synthase were not affected by the mutation. Therefore, it is stressed that the function of BEIIb cannot be complemented by BEIIa and BEI. These results strongly suggest that BEIIb plays a specific role in the transfer of short chains, which might then be extended by SS to form the A and B(1) chains of amylopectin cluster in rice endosperm.

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

The amylose-extender (Ae) gene encoding starch-branching enzyme IIb (SBEIIb) in maize is predominantly expressed in endosperm and embryos during kernel development. A maize genomic DNA fragment (-2964 to +20,485) containing the Ae gene was isolated and sequenced. The maize Ae mRNA is derived from 22 exons distributed over 16,914 bp. Twenty-one introns, differing in length from 76 bp to 4020 bp, all have conserved junction sequences (GT..AG). Sequence analysis of the 5'- and 3'-flanking regions revealed a consensus TATA-box sequence located 28 bp upstream of the transcription initiation site as determined by primer extension analysis, and a putative polyadenylation signal observed 29 bp upstream of the polyadenylation site based on cDNA sequence. Genomic Southern blot analysis suggests that a single Ae gene is present in the maize genome. Promoter activity was confirmed by testing a transcriptional fusion of the Ae 5'-flanking region between -2964 and +100 to a luciferase reporter gene in a transient expression assay using maize endosperm suspension cultured cells. 5' deletion analysis revealed that the 111 bp region from -160 to -50 is essential for high-level promoter activity.

Independent genetic control of maize starch-branching enzymes IIa and IIb. Isolation and characterization of a Sbe2a cDNA

In maize (Zea mays L.) three isoforms of starch-branching enzyme (SBEI, SBEIIa, and SBEIIb) are involved in the synthesis of amylopectin, the branched component of starch. To isolate a cDNA encoding SBEIIa, degenerate oligonucleotides based on domains highly conserved in Sbe2 family members were used to amplify Sbe2-family cDNA from tissues lacking SBEIIb activity. The predicted amino acid sequence of Sbe2a cDNA matches the N-terminal sequence of SBEIIa protein purified from maize endosperm. The size of the mature protein deduced from the cDNA also matches that of SBEIIa. Features of the predicted protein are most similar to members of the SBEII family; however, it differs from maize SBEIIb in having a 49-amino acid N-terminal extension and a region of substantial sequence divergence. Sbe2a mRNA levels are 10-fold higher in embryonic than in endosperm tissue, and are much lower than Sbe2b in both tissues. Unlike Sbe2b, Sbe2a-hybridizing mRNA accumulates in leaf and other vegetative tissues, consistent with the known distribution of SBEIIa and SBEIIb activities.

Allelic Analysis of the Maize amylose-extender Locus Suggests That Independent Genes Encode Starch-Branching Enzymes IIa and IIb

Starch branching enzymes (SBE) catalyze the formation of [alpha]-1,6-glucan linkages in the biosynthesis of starch. Three distinct SBE isoforms have been identified in maize (Zea mays L.) endosperm, SBEI, IIa, and IIb. Independent genes have been identified that encode maize SBEI and IIb; however, it has remained controversial as to whether SBEIIa and IIb result from posttranscriptional processes acting on the product of a single gene or whether they are encoded by separate genes. To investigate this question, we analyzed 16 isogenic lines carrying independent alleles of the maize amylose-extender (ae) locus, the structural gene for SBEIIb. We show that 22 d after pollination ae-B1 endosperm expressed little Sbe2b (ae)-hybridizing transcript, and as expected, ae-B1 endosperm also lacked detectable SBEIIb enzymatic activity. Significantly, we show that ae-B1 endosperm contained SBEIIa enzymatic activity, strongly supporting the hypothesis that endosperm SBEIIa and IIb are encoded by separate genes. Furthermore, we show that in addition to encoding the predominant Sbe2b-hybridizing message expressed in endosperm, the ae gene also encodes the major Sbe2b-like transcript expressed in developing embryos and tassels.

Expression of branching enzyme I of maize endosperm in Escherichia coli

The gene encoding for mature branching enzyme (BE) I (BEI) of maize (Zea mays L.) endosperm has been expressed in Escherichia coli using the T7 promoter. The expressed BEI was purified to near homogeneity so that amylolytic activity and bacterial BE could be completely eliminated from the BE preparation. The recombinant enzyme showed properties very similar to those of BEI purified from developing maize endosperm with respect to branching amylose and amylopectin. This result confirmed our earlier report that maize endosperm BEI had a higher rate of branching amylose and a much lower rate (less than 10% of that of branching amylose) of branching amylopectin. This study also showed a great advantage in purifying BEI from the bacterial expression system rather than from developing maize endosperm. Most important, this study has established the system with which to study the structure-function relationships of the maize BEI using site-directed mutagenesis.

Genetic Isolation, Cloning, and Analysis of a Mutator-Induced, Dominant Antimorph of the Maize amylose extender1 Locus

We report the genetic identification, molecular cloning, and characterization of a dominant mutant at the amylose extender1 locus, Ae1-5180. The identities of our clones are corroborated by their ability to reveal DNA polymorphisms between seven wild-type revertants from Ae1-5180 relative to the Ae1-5180 mutant allele and between four of five independently derived, Mutator (Mu)-induced recessive ae1 alleles relative to their respective wild-type progenitor alleles. The Ae1-5180 mutation is associated with two Mu1 insertions flanked by complex rearrangements of ae1-related sequences. One of the Mu1 elements is flanked by inverted repeats of ae1-related DNA of at least 5.0 kb in length. This Mu1 element and at least some of this flanking inverted repeat DNA are absent or hypermethylated in six of seven wild-type revertants of Ae1-5180 that were analyzed. The second Mu1 element is flanked on one side by the 5.0-kb ae1-specific repeat and on the other side by a sequence that does not hybridize to the ae1-related repeat sequence. This second Mu1 element is present in revertants to the wild type and does not, therefore, appear to affect ae1 gene function. A 2.7-kb ae1 transcript can be detected in wild-type and homozygous ae1-Ref endosperms 20 days after pollination. This transcript is absent in endosperms containing one, two, or three doses of Ae1-5180. This result is consistent with a suppression model to explain the dominant gene action of Ae1-5180 and establishes Ae1-5180 as an antimorphic allele. Homozygous wild-type seedlings produce no detectable transcript, indicating some degree of tissue specificity for ae1 expression. Sequence analyses establish that ae1 encodes starch branching enzyme II.

Differentiation of the Properties of the Branching Isozymes from Maize (Zea mays)

The multiple forms of branching enzyme (BE) from developing maize (Zea mays) endosperm were purified by modification of previous procedures such that amylase activity could be eliminated completely from the BE preparation. Three distinct assays for BE activity (phosphorylase a stimulation assay, BE linkage assay, and iodine stain assay) were used to characterize and differentiate the properties of the BE isoforms. This study presents the first evidence that the BE isoforms differ in their action on amylopectin. BEI had the highest activity in branching amylose, but its rate of branching amylopectin was less than 5% of that of branching amylose. Conversely, BEII isoforms had lower rates in branching amylose (about 9-12% of that of BEI) and had higher rates of branching amylopectin (about 6-fold) than BEI. The implication of these findings to the mechanism of amylopectin synthesis in vivo are discussed.

Comparison of soluble starch synthases and branching enzymes from leaves and kernels of normal and amylose-extender maize

Soluble starch synthases (SS) and branching enzymes (BE) from 20-day-old maize leaves and 22-day-old seeds of normal and amylose-extender (ae) were purified by DEAE-cellulose chromatography. Elution profiles of leaf extracts showed one major SS and two BE fractions from both genotypes. The SS fractions from normal and ae leaf extracts were capable of citrate-stimulated starch synthesis and had different reaction rates with various primers. The two BE fractions from normal leaf extracts differed significantly from each other but not when compared to the same BE from ae. Comparison of BE fractions from ae and normal leaves showed no differences based on chromatographic, kinetic, and immunological properties. Comparison of the leaf enzymes with endosperm enzymes showed major differences. Leaf extracts did not contain SSII or BEIIb observed in endosperm extracts. Developing ae endosperm lacks BEIIb activity and ae is the structural gene for BEIIb. The tissue specific expression of BEIIb in the endosperm provides the basis for explaining the tissue-specific expression of ae. We propose that as BEIIb is expressed in the endosperm, but not leaves, allelic substitution at the ae locus modifies only endosperm starch synthesis.

Chorismate Mutase Isoenzymes from Selected Plants and Their Immunological Comparison with the Isoenzymes from Sorghum bicolor

The isoenzyme pattern of chorismate mutase (EC 5.4.99.5) was examined by diethylaminoethyl-cellulose chromatography in a wide variety of plants. All plants contained a regulated form of chorismate mutase (CM-1), and most contained an additional, unregulated form (CM-2). The regulatory properties of CM-1 differed significantly between plants. Antisera prepared against CM-1 and CM-2 from Sorghum bicolor were used to test immunological cross reaction of chorismate mutases from other plants. There was a high degree of similarity between chorismate mutase isoenzymes from Sorghum bicolor and Zea mays and some with Hordeum vulgare, but all other species studied were antigenically distinct from sorghum. No homology between the structure of CM-1 and CM-2 was detected within any species.

Starch Branching Enzymes from Maize : Immunological Characterization using Polyclonal and Monoclonal Antibodies

Spleen cells from mice immunized with starch branching enzymes were fused with cells from the mouse myeloma Sp2/0-AG14 cell line to form hybridomas. Those hybridomas producing antibodies against the branching enzyme were screened by the enzyme-linked immunosorbent assay using purified branching enzyme as the antigen. Three monoclonal cell lines (1A1D7, 1A1C3 and 4D2A9D8) were found to produce antibodies which showed positive enzyme-linked immunosorbent assay reactions with maize branching enzyme I in addition to branching enzymes IIa and IIb. Three other monoclonal cell lines (4D2D10, 4D2F9, and 2A6C12) were also selected which were found to produce antibodies showing positive enzyme-linked immunosorbent assay reactions with branching enzymes IIa and IIb only.Amino acid composition and peptide maps obtained after trypsin or chymotrypsin digestion show that there is no difference between branching enzyme IIa and IIb but they are significantly different from branching enzyme I which, along with immunological data, suggests that only two forms of starch branching enzyme may be present in maize kernels.Immunological cross-reaction was also found between the starch branching enzyme from maize kernels and the glycogen branching enzyme from Escherichia coli using polyclonal antibodies against starch branching enzyme I or IIa and IIb or E. coli glycogen branching enzyme, suggesting some immunological similarities between maize starch branching enzymes and E. coli glycogen branching enzyme.