Allelic variation and differential expression at the 27-kilodalton zein locus in maize

Organ-specific variability and inheritance of maize proteins revealed by two-dimensional electrophoresis

Using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), the genetic variation of proteins was investigated in three organs (mesocotyl, sheath and blade of second leaf) from two maize lines and their hybrids. Nine hundred and eighty-six spots were numbered over the three organs. One hundred and fifty-five polypeptides were found to be genetically variable, due to allelic polymorphism of structural genes and/or to polymorphism of any genetic elements controlling protein amounts. Of these 155 variants 12% clearly showed complete dominance effects in the hybrid patterns, which could reveal dominance effects in the regulation of the protein biosynthesis. Comparison of the three organs showed that (i) the level of variability between lines depended upon the organ, since it varied from 7·5% for the blade to 12·6% for the mesocotyl and 13·2% for the sheath; (ii) 68 polypeptides displayed different kinds of variation in different organs and (iii) in all cases but one the dominant inheritance was organ-specific.

Duplication-Dependent CG Suppression of the Seed Storage Protein Genes of Maize

This study investigates the prevalence of CG and CNG suppression in single- vs. multicopy DNA regions of the maize genome. The analysis includes the single- and multicopy seed storage proteins (zeins), the miniature inverted-repeat transposable elements (MITEs), and long terminal repeat (LTR) retrotransposons. Zein genes are clustered on specific chromosomal regions, whereas MITEs and LTRs are dispersed in the genome. The multicopy zein genes are CG suppressed and exhibit large variations in CG suppression. The variation observed correlates with the extent of duplication each zein gene has undergone, indicating that gene duplication results in an increased turnover of cytosine residues. Alignment of individual zein genes confirms this observation and demonstrates that CG depletion results primarily from polarized C:T and G:A transition mutations from a less to a more extensively duplicated gene. In addition, transition mutations occur primarily in a CG or CNG context suggesting that CG suppression may result from deamination of methylated cytosine residues. Duplication-dependent CG depletion is likely to occur at other loci as duplicated MITEs and LTR elements, or elements inserted into duplicated gene regions, also exhibit CG depletion.

Characterization of the maize prolamin box-binding factor-1 (PBF-1) and its role in the developmental regulation of the zein multigene family

A maize prolamin box (P-box)-binding factor (PBF-1) has been purified and characterized from immature endosperm tissue. PBF-1 has a molecular weight of 38kDa. It is detected only in endosperm, but not in root or leaf tissues, consistent with its tissue-specific function. Site-directed mutagenesis experiments reveal that both the P-box and its flanking sequences are important for PBF-1 DNA binding. Developmental studies show that PBF-1 accumulates in the endosperm from 8 to at least 30days after pollination (DAP). From 16 to 24DAP, however, multiple shifted bands of protein(s)-DNA complexes can be observed, which correlate with an increase in zein gene expression. PBF-1 can also bind to the P-box from '22-kDa' and '19-kDa' zein promoters, but at a lower affinity than to the '27-kDa' zein promoter. The effects of protein dephosphorylation and zinc ion chelators on PBF-1 DNA binding activity are also shown. A model is proposed where PBF-1 serves as a 'recruiter' of class-specific transcription factors like Opaque2 (O2).

Zeon-1, a member of a new maize retrotransposon family

We have previously shown that the tandemly duplicated 27 kDa maize storage protein locus underwent mitotic rearrangement to yield a single-copy allele in isolates of the inbred line A188. This rearrangement contains a new LTR retrotransposon, designated Zeon-1. This middle repetitive element of 7313 bp had two long terminal repeats, a primer binding site, a polypurine tract and a gag-related open reading frame of 375 amino acids. Transcripts of the gag-related region were detected by the polymerase chain reaction (PCR) in certain maize tissues, and Western blots detected the gag-related protein in the same tissues. Moreover, the product of this mitotic rearrangement was shown to contain the same insertion site and 3' LTR as Zeon-1, suggesting that this rearrangement occurs with unusual precision. Zeon elements were found to be present in teosinte and not present in the Gramineae wheat, barley, sorghum and rye.

Identification of two opaque2 modifier loci in quality protein maize

Genetic modifiers of opaque2 convert the soft, starchy endosperm of opaque2 maize mutants to a hard, vitreous phenotype, while maintaining the enhanced lysine content of the grain. Genetic analysis of F2 segregating seeds from crosses of opaque2 by modified opaque2 genotypes indicated that the modifiers are complex traits that act codominantly. We developed two different segregating F2 populations and mapped the modifier loci by restriction fragment length polymorphism (RFLP) analysis. A relationship was found between formation of vitreous endosperm and the locus encoding the gamma-zein storage protein, which maps near the centromere of chromosome 7. Endosperm modification was consistently associated with the presence of two rather than one gamma-zein gene at this locus. A second modifier locus was mapped near the telomere of chromosome 7L.

Structural characterization and promoter activity analysis of the gamma-kafirin gene from sorghum

A genomic clone encoding the gamma-kafirin gene from sorghum was isolated and sequenced. A 2938 bp sequenced fragment includes an intronless open reading frame of 636 nucleotides encoding a putative polypeptide of 212 amino acids. Comparison of the deduced amino acid sequence of gamma-kafirin with the published sequences of gamma-prolamins of maize, and Coix revealed highly conserved domains. The N-terminal region of these proteins contains the conserved hexapeptide PPPVHL, which is repeated eight times in gamma-zein, four times in gamma-kafirin and three times in gamma-coixin. The number of PPPVHL repeats accounts predominantly for the differences in the molecular weights of gamma-prolamins. Several putative regulatory sequences common to the gamma-kafirin and gamma-zein genes were identified in both the 5' and the 3' flanking regions. Putative GCN4-like regulatory sequences were found at positions -192 and -476 in the 5' flanking region of gamma-kafirin. In the 3' noncoding region, three putative polyadenylation signals, two AATAAT and one AATGAA, were found at positions +658, +716, and +785, respectively. In order to investigate the role of the putative GCN4-like motifs and other possible cis-acting element(s) of the gamma-kafirin promoter, a series of deleted and chimeric promoter constructs were introduced into maize, Coix and sorghum tissues by particle bombardment. Histochemical analysis of beta-glucuronidase (GUS) activity in different tissues indicated that the element(s) responsible for tissue specificity is probably located in the 285-bp proximal region of the promoter, while the remaining promoter sequence seems to carry the element(s) responsible for the quantitative response.

Sequence analysis of 22 kDa-like alpha-coixin genes and their comparison with homologous zein and kafirin genes reveals highly conserved protein structure and regulatory elements

Several genomic and cDNA clones encoding the 22 kDa-like alpha-coixin, the alpha-prolamin of Coix seeds, were isolated and sequenced. Three contiguous 22 kDa-like alpha-coixin genes designated alpha-3A, alpha-3B and alpha-3C were found in the 15 kb alpha-3 genomic clone. The alpha-3A and alpha-3C genes presented in-frame stop codons at position +652. The two genes with truncated ORFs are flanking the alpha-3B gene, suggesting that the three alpha-coixin genes may have arisen by tandem duplication and that the stop codon was introduced before the duplication. Comparison of the deduced amino acid sequences of alpha-coixin clones with the published sequences of 22 kDa alpha-zein and 22 kDa-like alpha-kafirin revealed a highly conserved protein structure. The protein consists of an N-terminus, containing the signal peptide, followed by ten highly conserved tandem repeats of 15-20 amino acids flanked by polyglutamines, and a short C-terminus. The difference between the 22 kDa-like alpha-prolamins and the 19 kDa alpha-zein lies in the fact that the 19 kDa protein is exactly one repeat motif shorter than the 22 kDa proteins. Several putative regulatory sequences common to the zein and kafirin genes were identified within both the 5' and 3' flanking regions of alpha-3B. Nucleotide sequences that match the consensus TATA, CATC and the ca. -300 prolamin box are present at conserved positions in alpha-3B relative to zein and kafirin genes. Two putative Opaque-2 boxes are present in alpha-3B that occupies approximately the same positions as those identified for the 22 kDa alpha-zein and alpha-kafirin genes. Southern hybridization, using a fragment of a maize Opaque-2 cDNA clone as a probe, confirmed the presence of Opaque-2 homologous sequences in the Coix and sorghum genomes. The overall results suggest that the structural and regulatory genes involved in the expression of the 22 kDa-like alpha-prolamin genes of Coix, sorghum and maize, originated from a common ancestor, and that variations were introduced in the structural and regulatory sequences after species separation.

Analyses of genes that encode the 15-kDa zein protein of maize: identification of potential gene regulatory elements

A gene (gZ15.4.1) encoding the 15-kDa zein polypeptide was isolated from maize cultivar A5707, and its nucleotide sequence was determined. A total of 2085 bp was sequenced, including about 300 bp of 5'-flanking DNA that includes several potential regulatory elements not available in the previously published 15-kDa zein-encoding gene (gZ15A) sequence. Several nt differences between gZ15.4.1 and gZ15A were observed, which include two single amino acid replacements.

Corn kernel cysteine proteinase inhibitor as a novel cystatin superfamily member of plant origin. Molecular cloning and expression studies

A full-length cDNA clone for a cysteine proteinase inhibitor (cystatin) was isolated from a lambda gt10 cDNA library of immature corn kernels by screening with a mixture of cDNA inserts for oryzacystatins I and II. The cDNA clone spans 960 base pairs, encoding a 135-amino-acid protein containing a signal peptide fragment. The protein, named corn cystatin I, is considered to be a member of the cystatin superfamily, since it contains the commonly conserved Gln-Val-Val-Ala-Gly region that exists in most known cystatins as a probable binding site and is significantly similar to other cystatins in its overall amino acid sequence. Corn cystatin I expressed in Escherichia coli showed a strong papain-inhibitory activity. Northern blot analysis showed that the amount of mRNA for corn cystatin I reaches a maximum 2 weeks after flowering and then decreases gradually.

Genomic organization of an alpha-zein gene cluster in maize

The genes encoding the alpha-zein proteins of maize constitute a large multigene family of some 75 genes. This multigene family can be divided into four subfamilies based on the nucleotide sequences of their genes and the deduced amino acid sequences of their proteins. We describe for the first time evidence of a clustering of five alpha-zein subfamily 4 (SF4) genes that are members of one of the major alpha-zein subfamilies in a 56 kb region of the genome of the maize inbred line W22. None of the other three known alpha-zein gene subfamilies (SF1, SF2, or SF3) are present in this cluster. The genomic region was reconstructed using restriction endonuclease maps to identify and align three overlapping cosmid clones isolated from a genomic library. The alpha-zein genes are not evenly spaced; the minimum distance between genes is 3.5 kb; the maximum is 13 kb. All the alpha-zein genes in the cluster have the same transcriptional orientation. The location and sequences of some of the repetitive DNA elements in this gene cluster were determined. We estimate that there are a minimum of eight repetitive DNA elements in this region. The sequences of the repetitive elements (not functionally defined) are located between or among the alpha-zein genes. The regions containing two of these repetitive elements (Rep1 and Rep4) have been sequenced; they are about 15 kb apart in the genome. These repetitive elements have similar sequences for about 300 bp out of the 400 bp compared. The regions of sequence similarity, however, are in reverse orientation to one another.(ABSTRACT TRUNCATED AT 250 WORDS)

Sequence variation between alleles reveals two types of copy correction at the 27-kDa zein locus of maize

In many inbred lines of maize, two 27-kDa storage protein (zein) genes are found within tandem duplications of 12 kb. Both genes of the duplicated allele from the maize inbred line A188 were sequenced and compared to a similar duplicated allele in another inbred line, W22, and to a single-copy allele in the inbred line W64A. The comparisons reveal interesting patterns in the distribution of sequence changes between these alleles. Differences between the two duplicated alleles that are conserved between the two genes of each allele are found exclusively in the 5' region. In contrast, differences between the individual genes of each allele in the 3' region are conserved between the two alleles. The first case is indicative of an intraallelic copy correction mechanism, whereas the second may result from interallelic copy correction. These may be mediated by gene conversion processes, as previously described for other multigene families.

opaque-2 modifiers increase gamma-zein synthesis and alter its spatial distribution in maize endosperm

Through the action of opaque-2 modifier genes, the soft, floury endosperm of opaque-2 mutants is converted to a vitreous phenotype. This change in endosperm texture is associated with a twofold to threefold increase in gamma-zein content. To investigate the effect of opaque-2 modifiers on the expression of gamma-zein genes, we analyzed the synthesis and distribution of gamma-zein protein and the level of gamma-zein mRNAs in developing endosperms of the inbreds W64A and W64Ao2, a modified opaque-2 mutant Pool 34 QPM, and their reciprocal F1 hybrids. We also characterized the number and organization of gamma-zein genes in these and related maize genotypes. Our studies show that opaque-2 modifiers are semidominant genes, resulting in a twofold to threefold increase in gamma-zein gene expression in both opaque-2 and normal genetic backgrounds. The increase in gene expression appears to be a consequence of enhanced mRNA transcription or stability rather than gene amplification because gamma-zein genes occur in one or two copies in modified as well as nonmodified genetic backgrounds. Ultrastructural studies showed that gamma-zein occurs in high concentrations in the first few subaleurone cells of nonmodified endosperms, but high concentrations of gamma-zein occur in the subaleurone and central endosperm cells of modified opaque-2 mutants. The increased concentration and distribution of gamma-zein in modified endosperms are highly correlated with the activity of opaque-2 modifier genes.

A homologous expression system for cloned zein genes

Expression of the genes encoding the 10-, 15-, and 27-kDa zeins is maintained in suspension cultures derived from developing endosperm tissue of maize (Zea mays L.). Although expression of these genes is reduced in endosperm cultures as compared with that in endosperm tissue from developing kernels, it remains specific to the origin of explant, since no transcripts are detected in leaf tissue-derived suspension cultures. Transcript sizes are identical to those in developing seed endosperm tissue. Furthermore, accurate transcription initiation of the 10- and 27-kDa zein genes is observed by S1 nuclease mapping. Protoplasts isolated from endosperm cultures are capable of expressing foreign genes when transfected by electroporation. We demonstrate that the 5' flanking sequences of the 10- and 27-kDa zein genes are capable of promoting chloramphenicol acetyltransferase (CAT) gene expression in these transfected protoplasts. Our observations show that these maize endosperm cultures can be used as an efficient homologous system to study transcriptional regulation of zein genes.

Post-transcriptional regulation of methionine content in maize kernels

Message levels for a methionine-rich 10 kDa zein were determined in three inbred lines of maize and their reciprocal crosses at various stages during endosperm development. Inbred line BSSS-53, which overexpresses the 10 kDa protein in mature kernels, was shown to have higher mRNA levels in developing endosperm, as compared to inbred lines W23 and W64A. Differences in mRNA levels could not be explained by differences in transcription rate of the 10 kDa zein gene, indicating differential post-transcriptional regulation of this storage protein in the different inbred lines analyzed. Among progeny segregating for the BSSS-53 allele of the 10 kDa zein structural gene Zps10/(22), mRNA levels are independent of Zps10/(22) segregation, indicating that post-transcriptional regulation of mRNA levels takes place via a trans-acting mechanism. In the same progeny, mRNA levels are also independent of allelic segregation of the regulatory locus Zpr10/(22). Thus, the trans-acting factor encoded by Zpr10/(22) determines accumulation of 10 kDa zein at a translational or post-translational step. Multiple trans-acting factors are therefore involved in post-transcriptional regulation of the methionine-rich 10 kDa zein.

Positional cues and differential gene expression in somatic embryos of higher plants

Much of the organization of higher vascular plants is determined during the formation of the embryo. In addition to the zygotic embryo which results from sexual fertilization in the ovule, many plants are capable of producing embryos from somatic cells. Of particular interest to plant developmental biologists is the phenomenon of somatic embryogenesis in cultures of the domesticated carrot which, because of its tractable nature in experimental manipulations, is presently regarded as a suitable model for studying pattern formation in plants. This short review considers the state of our knowledge concerning the origin and perception of positional information in plant embryos, and the temporal and spatial expression of genes. The available data provide a number of promising leads for cell-cell interactions in embryos, and there are some clear indications that the spatial distribution of certain gene products is correlated with changes in morphology. However, there is, as yet, insufficient evidence with which to forge a link between positional cues and the expression of genes which influence developmental transitions in embryos.

Genetic analysis of methionine-rich storage protein accumulation in maize

Experiments were conducted to determine the chromosomal location of the gene conditioning overproduction of a methionine-rich, 10-K zein in maize kernels of line BSSS53. In addition, the chromosomal location of the structural gene encoding the overproduced protein was determined. Whereas the structural gene, designated Zps10/(22), was found to be located on the long arm of chromosome 9 near the centromere, the locus regulating overproduction of the zein protein was mapped to the short arm of chromosome 4. This regulatory gene has been designated Zpr10/(22). Regulation of 10-K zein production by Zpr10/(22) is, therefore, via a trans-acting mechanism.

The synthesis of a 19 kilodalton zein protein in transgenic petunia plants

Transcriptional fusions composed of a 19 kilodalton zein cDNA, the 5' flanking region from a beta-phaseolin gene, and 3' flanking regions from either the phaseolin or a 15-kilodalton zein gene were introduced into Petunia by Agrobacterium-mediated transformation. The expression of both zein mRNA and protein in these transgenic plants was seed-specific and developmentally regulated. Both monocot (zein) and dicot (phaseolin) polyadenylation consensus sequences were recognized in Petunia. Analysis by immunoblotting showed that the M(r) of the zein protein corresponded to that of the mature protein, suggesting that recognition and cleavage of the signal sequence had occurred. While zein mRNA accumulated to approximately 1% of the total poly(A)(+) RNA in seeds of the transformed plants, zein protein was present at a much lower concentration than expected, at most being 0.005% of the total seed protein. These results suggest that the 19 kilodalton zein gene, in addition to lacking specific sequences required for efficient transcription in dicots, might also lack sequences required for the efficient synthesis, targeting, transport, or stabilization of the protein.

Isolation and sequence of a gene encoding a methionine-rich 10-kDa zein protein from maize

We have isolated the gene encoding a methionine-rich 10-kDa zein protein from a lambda EMBL3 maize genomic 'mini' library of the inbred line BSSS-53 and determined its nucleotide sequence. The sequence matches perfectly with a cDNA clone from the inbred line W22 (which has the same restriction fragment length polymorphism as many inbred lines tested) indicating that we have isolated a functional storage protein gene that is very conserved in maize. This comparison also excludes any splicing of any precursor mRNA and therefore any presence of introns. A number of potential regulatory sequences have been located in the flanking regions. The 10-kDa-zein gene represents the last size class in the zein multigene family to be characterized. Its structure allows us now to re-examine the relationship of all the zein proteins and also to compare the structure of a new class of storage proteins that are rich in methionine, an essential amino acid in livestock fodder.

Transgenes as probes for active chromosomal domains in mouse development

Embryonic development entails a well defined temporal and spatial programme of gene expression, which may be influenced by active chromosomal domains. These chromosomal domains can be detected using transgenes which integrate randomly throughout the genome, as their expression can be affected by chromosomal position. Position effects are probably exerted most strongly on transgenes that do not contain strong promoters, enhancers or other modulating sequences. Here we have systematically explored position effects using a transgene with the weak herpes-simplex-virus thymidine-kinase promoter, linked to the readily visualized lacZ indicator gene (HSV-TK-lacZ). Each transgenic fetus with detectable expression displayed a unique lacZ staining pattern. Thus expression of this construct is apparently dictated entirely by its chromosomal position, without any construct specificity. Furthermore the transgene is faithfully transmitted to subsequent generations, allowing for systematic mapping of changes in expression during development and in adult life. These results demonstrate that transgenes can indeed be powerful tools to probe the genome for active chromosomal regions, with the potential for identifying endogenous genes involved in organogenesis and pattern formation.

Differential expression of a gene for a methionine-rich storage protein in maize

A methionine-rich 10 kDa zein storage protein from maize was isolated and the sequence of the N-terminal 30 amino acids was determined. Based on the amino acid sequence, two mixed oligonucleotides were synthesized and used to probe a maize endosperm cDNA library. A full-length cDNA clone encoding the 10 kDa zein was isolated by this procedure. The nucleotide sequence of the cDNA clone predicts a polypeptide of 129 amino acids, preceded by a signal peptide of 21 amino acids. The predicted polypeptide is unique in its extremely high content of methionine (22.5%). The maize inbred line BSSS-53, which has increased seed methionine due to overproduction of this protein, was compared to W23, a standard inbred line. Northern blot analysis showed that the relative RNA levels for the 10 kDa zein were enhanced in developing seeds of BSSS-53, providing a molecular basis for the overproduction of the protein. Southern blot analysis indicated that there are one or two 10 kDa zein genes in the maize genome.