Characterization of a null-allele for the Gy 4 glycinin gene from soybean

Haplotype Analysis and Linkage Disequilibrium at Five Loci in Eragrostis tef

Eragrostis tef (Zucc.), a member of the Chloridoideae subfamily of grasses, is one of the most important food crops in Ethiopia. Lodging is the most important production problem in tef. The rht1 and sd1 dwarfing genes have been useful for improving lodging resistance in wheat and rice, respectively, in what has been known as the “Green Revolution.” All homologs of rht1 and sd1 were cloned and sequenced from 31 tef accessions collected from across Ethiopia. The allotetraploid tef genome was found to carry two rht1 homologs. From sequence variation between these two putative homologs, an approximate ancestral divergence date of 6.4 million years ago was calculated for the two genomes within tef. Three sd1 homologs were identified in tef, with unknown orthologous/paralogous relationships. The genetic diversity in the 31 studied accessions was organized into a relatively small number of haplotypes (2−4) for four of these genes, whereas one rht1 homeologue exhibited 10 haplotypes. A low level of nucleotide diversity was observed at all loci. Linkage disequilibrium analysis demonstrated strong linkage disequilibrium, extending the length of the five genes investigated (2−4 kb), with no significant decline. There was no significant correlation between haplotypes of any of these genes and their recorded site of origin.

Molecular analysis of glycinin genes in soybean mutants for development of gene-specific markers

Soybean mutant lines that differ in 11S glycinin and 7S β-conglycinin seed storage protein subunit compositions were developed. These proteins have significant influence on tofu quality. The molecular mechanisms underlying the mutant lines are unknown. In this study, gene-specific markers for five of the glycinin genes (Gy1 to Gy5) were developed using three 11S null lines, two A(4) null Japanese cultivars, Enrei and Raiden, and a control cultivar, Harovinton. Whereas gene-specific primers produced the appropriate products in the control cultivar for the Gy1, Gy2, Gy3 and Gy5 genes, they did not amplify in mutants missing the A(1a)B(2), A(2)B(1a), A(1b) B(1b), and A(3)B(4) subunits. However, ecotype targeting induced local lesions in genomes (EcoTILLING) and sequencing analysis revealed that the absence of the A(4) peptide in the mutants is due to the same point mutation as that in Enrei and Raiden. Selection efficiency of the gene-specific primer pairs was tested using a number of breeding lines segregating for the different subunits. Primer pairs specific to each of the Gy1, Gy2, Gy3, and Gy5 genes can be used to detect the presence or absence of amplification in normal or mutant lines. The Gy4 null allele can be selected for by temperature-switch PCR (TS-PCR) for identification of the A(4) (G4) null genotypes. In comparison to protein analysis by SDS-PAGE, gene-specific markers are easier, faster and more accurate for analysis, they do not have to use seed, and can be analyzed at any plant growth stage for marker-assisted selection.

In vitro and in situ antimicrobial action and mechanism of glycinin and its basic subunit

Glycinin, basic subunit and β-conglycinin were isolated from soybean protein isolate and tested for their antimicrobial action against pathogenic and spoilage bacteria as compared to penicillin. The three fractions exhibited antibacterial activities equivalent to or higher than penicillin in the next order; basic subunit>glycinin>β-conglycinin with MIC of 50, 100 and 1000 μg/mL, respectively. The IC(50%) values of the basic subunit, glycinin and β-conglycinin against Listeria\monocytogenes were 15, 16 and 695 μg/mL, against Bacillussubtilis were 17, 20, and 612 μg/mL, and against S. Enteritidis were 18, 21 and 526 μg/mL, respectively. Transmission electron microscopy images of L. monocytogenes and S. Enteritidis exhibited bigger sizes and separation of cell wall from cell membrane when treated with glycinin or basic subunit. Scanning electron microscopy of B. subtilis indicated signs of irregular wrinkled outer surface, fragmentation, adhesion and aggregation of damaged cells or cellular debris when treated with glycinin or the basic subunits but not with penicillin. All tested substances particularly the basic subunit showed increased concentration-dependent cell permeation assessed by crystal violet uptake. The antimicrobial action of glycinin and basic subunit was swifter than that of penicillin. The cell killing efficiency was in the following descending order; basic subunit>glycinin>penicillin>β-conglycinin and the susceptibility of the bacteria to the antimicrobial agents was in the next order: L. monocytogenes>B. Subtilis>S. Enteritidis. Adding glycinin and the basic subunit to pasteurized milk inoculated with the three bacteria; L. monocytogenes, B. Subtilis and S. Enteritidis (ca. 5 log CFU/mL) could inhibit their propagation after 16-20 days storage at 4 °C by 2.42-2.98, 4.25-4.77 and 2.57-3.01 log and by 3.22-3.78, 5.65-6.27 and 3.35-3.72 log CFU/mL, respectively.

Identification of several gy4 nulls from the USDA soybean germplasm collection provides new genetic resources for the development of high-quality tofu cultivars

Tofu, a cheese-like food made by curdling soy milk, is a major dietary staple of Asian countries. Consumption of tofu and other soy products is steadily increasing in North America due to its well-known health benefits. Soybean A(5), A(4), and B(3) peptide null lines 'Enrei' and 'Raiden' are commonly utilized in breeding programs to develop high-quality tofu cultivars. To expand the genetic diversity it is desirable to identify and utilize other A(5), A(4), and B(3) null genotypes in the development of improved tofu cultivars that are adapted to North American conditions. In this study were screened diverse soybean accessions from the USDA Soybean Germplasm Collection to identify Gy4 mutants, the locus that controls A(5), A(4), and B(3) peptide production. Analysis of total seed proteins from 485 soybean lines by SDS-PAGE enabled the identification of 38 accessions that lacked the A(5), A(4), and B(3) peptides. These accessions showed marked differences in seed size and seed coat color and represented different maturity groups ranging from 0 to IX. To ascertain the molecular basis for the lack of A(5), A(4), and B(3) peptides in the newly identified Gy4 mutants, the nucleotide sequence of a portion of the Gy4 gene was determined from eight soybean accessions representing different maturity groups. These eight Gy4 mutants revealed a single point mutation that changed the translation initiation codon ATG to ATA, resulting in the A(5), A(4), and B(3) null phenotype. The newly identified Gy4 mutants from this study will enable plant breeders to expand the genetic diversity of North American food-quality soybeans and also aid in the development of hypoallergenic soybeans.

Evaluation of Glycine max mRNA clusters

BACKGROUND

Clustering the ESTs from a large dataset representing a single species is a convenient starting point for a number of investigations into gene discovery, genome evolution, expression patterns, and alternatively spliced transcripts. Several methods have been developed to accomplish this, the most widely available being UniGene, a public domain collection of gene-oriented clusters for over 45 different species created and maintained by NCBI. The goal is for each cluster to represent a unique gene, but currently it is not known how closely the overall results represent that reality. UniGene's build procedure begins with initial mRNA clusters before joining ESTs. UniGene's results for soybean indicate a significant amount of redundancy among some sequences reported to be unique mRNAs. To establish a valid non-redundant known gene set for Glycine max we applied our algorithm to the clustering of only mRNA sequences. The mRNA dataset was run through the algorithm using two different matching stringencies. The resulting cluster compositions were compared to each other and to UniGene. Clusters exhibiting differences among the three methods were analyzed by 1) nucleotide and amino acid alignment and 2) submitting authors conclusions to determine whether members of a single cluster represented the same gene or not.

RESULTS

Of the 12 clusters that were examined closely most contained examples of sequences that did not belong in the same cluster. However, neither the two stringencies of PECT nor UniGene had a significantly greater record of accuracy in placing paralogs into separate clusters.

CONCLUSION

Our results reveal that, although each method produces some errors, using multiple stringencies for matching or a sequential hierarchical method of increasing stringencies can provide more reliable results and therefore allow greater confidence in the vast majority of clusters that contain only ESTs and no mRNA sequences.

Single-nucleotide polymorphisms in soybean

Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson's theta was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r(2)) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

Soy glycinin: influence of pH and ionic strength on solubility and molecular structure at ambient temperatures

This study describes the relationship between the solubility of glycinin, a major soy protein, and its structural properties at a quaternary, tertiary, and secondary folding level under conditions representative for food products. When the ionic strength is lowered from 0.5 to 0.2 or 0.03, the basic polypeptides shift more to the exterior of the glycinin complex, as determined at pH 7.6 by labeling solvent-exposed lysines, supported by the study of the proteolytic action of clostripain on glycinin. This structural reorganization caused the pH of minimal solubility to shift to higher values. Ultracentrifugational analysis shows that at pH 7.6 and an ionic strength of 0.5 glycinin forms hexameric complexes (11S), whereas at pH 3.8 and at an ionic strength of 0.03 glycinin exists as trimers (7S). Intermediate situations are obtained by modulation of pH and ionic strength. The observed quaternary dissociation correlates with an increased amount of nonstructured protein at a secondary level and with changes in tertiary folding as determined using circular dichroism. Tryptophan fluorescence shows no significant structural changes for different ionic strengths but demonstrates a more tightly packed fluorophore environment when the pH is lowered from 7.6 to 3.8.

Nucleotide sequence analysis of a novel globulin1 null allele from the Illinois high protein strain of maize

The highly polymorphic maize globulin1 (glb1) gene encodes an abundant embryo storage protein. The present study extends the analysis of glb1 variants to further explore the nature of polymorphism at this locus. The null allele Glb1-N1Hb, derived from the Illinois High Protein (IHP) strain of maize was characterized at the molecular level by nucleotide sequence analysis. Among other differences, a single-base insertion leading to a premature termination codon in the carboxyl-terminal half of the otherwise normal protein was observed. The likely reasons for the absence of GLB1 protein accumulation in the IHP strain of maize are discussed.

Genetic mapping of the Gy4 and Gy5 glycinin genes in soybean and the analysis of a variant of Gy4

The predominant storage protein of soybean [Glycine max (L.) Merr.] seed is a globulin called glycinin. Thus far five genes encoding glycinin subunits have been described, and these are denoted by the gene symbols Gy1 to Gy5. The objectives of this study were to map two of these genes, Gy4 and Gy5, and to conduct a genetic analysis of a subunit size-variant from an allele of Gy4. For this purpose a population was formed with an interspecific cross between PI 468916 (G. soja) and A81-356022 (G. max). The two size forms of G4, the subunit from Gy4, segregated codominantly in the mapping population, and were due to a short insertion in the hypervariable region of the mutant protein. The biochemical and molecular characteristics of the two subunits indicate that they are produced from alternate alleles of the same gene. The gene symbols Gy (a) and Gy (b) have been assigned to the normal and variant genes, respectively. When genomic DNA from the two parents was probed with a Gy4 cDNA, RFLPs were identified for both Gy4 and Gy5. Using these genetic markers, the Gy4 and Gy5 glycinin genes were mapped in linkage group "O" and "F" on the public soybean genomic map.

The glycinin box: a soybean embryo factor binding motif within the quantitative regulatory region of the 11S seed storage globulin promoter

The soybean embryo factor binding sequence in the glycinin A2B1a gene promoter was delimited to an A/T-rich 9 bp sequence, 5'-TAATAATTT-3', designated as the glycinin box, by DNA footprinting and gel mobility shift assay using synthetic oligonucleotides. It was shown that the interaction with the factor takes place at a defined DNA sequence rather than at random A/T-rich sequence blocks in the glycinin 5' flanking region. There are four glycinin boxes in the quantitative regulatory region between positions -545 and -378 of the glycinin A2B1a promoter. Multiple nonamer motifs similar to the glycinin box were also found in the equivalent regions of other glycinin and legumin promoters, suggesting that they must be conserved as a binding site for the embryo factor that activates the differential and stage-specific expression of seed 11S globulin genes in leguminous plants.

mRNA surveillance by the Caenorhabditis elegans smg genes

mRNAs that contain premature stop codons are unstable in most eukaryotes, but the mechanism of their degradation is largely unknown. We demonstrate that functions of the six C. elegans smg genes are necessary for rapid turnover of nonsense mutant mRNAs of the unc-54 myosin heavy chain gene. Nonsense alleles of unc-54 express mRNAs that are unstable in smg(+) genetic backgrounds but have normal or near normal stability in smg(-) backgrounds. smg mutations also stabilize mRNA of unc-54(r293), a small deletion that removes the unc-54 polyadenylation site and expresses an aberrant mRNA. Most unc-54 nonsense mutations are recessive in both smg(+) and smg(-) genetic backgrounds. However, four specific alleles are recessive when smg(+) and dominant when smg(-). These smg-dependent dominant alleles express nonsense mutant polypeptides that disrupt thick filament and/or sarcomere assembly. All four alleles are predicted to express nonsense fragment polypeptides that contain most of the myosin globular head domain without an attached rod segment. By degrading messages that contain premature stop codons, the smg genes eliminate mRNAs that encode potentially toxic protein fragments. We propose that this system of mRNA turnover protects cells from their own errors of transcription, mRNA processing, or mRNA transport.

Characterization of a Gy4 glycinin gene from soybean Glycine max cv. forrest

The glycinin gene family encoding the glycinin subunits in soybean plants is composed of at least five gene members. A genomic clone lambda S312 containing the Gy4 gene from a genomic library of cv. Forrest was isolated and partially characterized. The organization of this gene was found to be similar to that of a null allele from cv. Raiden, but different from the Gy4 gene from cv. Dare. The complete nucleotide sequence of this gene has been determined. It is 2599 bp long consisting of four exons and three introns. Comparing the DNA sequences between this gene and the gene from Dare and a null allele from Raiden, the difference found in the coding region was 5'-GCAGTGCAAG-3' (nt 824 to 833) in the former case versus 5'-TGGAGTTGCAATT-3' (nt 1314 to 1326) in the latter case in the exon 2 domain, resulting in three amino acid differences and one amino acid absence. Some other differences were also found in the non-coding region. The coding sequence and 5'-flanking region of the Gy4 gene, when compared with that of other legumin genes as well as group 1 glycinin subunit genes, revealed some interesting features: (1) a transposable element-like sequence was found in the hypervariable region (HVR) of the exon 3 domain, which was lacking in the legumin and the glycinin group 1 genes; (2) in the 5'-flanking region from nt -145 to -1, two high-homology sequences were found: one from nt -141 to nt -132, the other from nt -118 to nt -92 which includes the 'legumin box' and the RY repeat element.

Synthesis and assembly of soybean beta-conglycinin in vitro

The construction of SP6-derived expression plasmids that encode normal and modified beta-conglycinin subunits is described. With the exception of an additional methionine at their NH2-terminal ends and the lack of glycans, the normal subunits synthesized at the direction of these plasmids corresponded to mature alpha and beta subunits isolated from soybean seeds. The subunits assembled into trimers in vitro that were equivalent in size to those formed in vivo. This result shows that the glycans are not required either for protein folding or oligomer assembly. Subunits produced from other plasmids, which had modifications in a highly conserved hydrophobic region in the COOH-terminal end of the subunits, either did not assemble or assembled at an extremely low rate compared to unmodified subunits. Structural changes at the more hydrophilic NH2-terminal end had mixed effects. Several subunits modified in this region assembled into trimers at rates that were either equal or greater than those for normal alpha subunits. Others assembled less completely than the normal subunits. Our results indicate that the in vitro synthesis and assembly assay will be useful in evaluating structure-function relationships in modified beta-conglycinin subunits. The results also show that structural changes at the NH2-terminal end of the subunits are tolerated to a greater extent than modifications in the hydrophobic conserved region in the COOH-terminal half of the subunits, and this information will be useful in efforts to improve soybean quality.

Characterization of the maize Globulin-2 gene and analysis of two null alleles

The most abundant proteins present in maize (Zea mays L.) embryos are saline-soluble globulins. A Mr 45,000 globulin component, designated GLB2, is encoded by the Glb2 gene. A cDNA clone corresponding to Glb2 was used as radiolabeled probe to examine the expression of Glb2 in developing embryos and other maize tissues. Glb2 transcripts accumulate during embryo development and are not detectable in germinating kernels. Glb2 transcripts are found only in the developing embryo, and not in endosperm, seedling, or unfertilized ears. Analysis of globulin profiles in embryos homozygous for either a previously described null allele, Glb-2-0, or a novel null allele, Glb2-N1, revealed that these embryos lack not only the GLB2 protein but also globulins of lower molecular mass which may represent processed forms of GLB2. Southern blot analysis of DNA from Glb2-0/0 and Glb2-N1/N1 plants in which a Glb2-specific clone is used as probe indicates that the two null alleles are genetically distinct.

Analysis of unstable RNA transcripts of insecticidal crystal protein genes of Bacillus thuringiensis in transgenic plants and electroporated protoplasts

We have examined expression of several insecticidal crystal protein (ICP) genes of Bacillus thuringiensis in transgenic tobacco plants and electroporated carrot protoplasts. We determined that low levels of lepidopteran toxin cryIA(b) ICP gene expression in plants and electroporated carrot cells is due to RNA instability. We used a series of 3' deleted by cryIA(b) constructs directed by the cauliflower mosaic virus 35S promoter to demonstrate that this instability is minimally contained in the first 579 bases of the gene in both systems. This instability may result from 5'----3' as well as 3'----5' RNA metabolism. The coleopteran toxic cryIIIA gene was also examined in electroporated carrot cells, and found to be poorly expressed. A model for improvement of ICP RNA stability in plants is presented.

Sequence analysis of two null-mutant alleles of the single Arabidopsis Adh locus

Data presented in this paper deal with a further molecular characterization of 2 out of 32 EMS-induced Arabidopsis ADH null mutants that we isolated previously. In order to localize and characterize each mutation at the molecular level, we have cloned and completely sequenced the R002 and R006 null mutant alleles. For mutant R002, which does not contain any detectable levels of ADH protein and mRNA, we have found that the mutation is due to a single C to T base pair substitution in the reading frame; this leads to the incorporation of a TAG stop codon (amber nonsense mutation). For mutant R006, which contains normal levels of inactive protein and mRNA levels, we found a G to A base pair transition. This gives rise to a Cys to Tyr amino acid substitution in the active site of the ADH enzyme.