Genes for zein subunits on maize chromosome 4

Eukaryotic peptide chain release factor 1 participates in translation termination of specific cysteine-poor prolamines in rice endosperm

Prolamines are alcohol-soluble proteins classified as either cysteine-poor (CysP) or cysteine-rich (CysR) based on whether they can be alcohol-extracted without or with reducing agents, respectively. In rice esp1 mutants, various CysP prolamines exhibit both reduced and normal amounts of isoelectric focusing bands, indicating that the mutation affects only certain prolamine classes. To examine the genetic regulation of CysP prolamine synthesis and accumulation, we constructed a high-resolution genetic linkage map of ESP1. The ESP1 gene was mapped to within a 20 kb region on rice chromosome 7. Sequencing analysis of annotated genes in this region revealed a single-nucleotide polymorphism within eukaryotic peptide chain release factor (eRF1), which participates in stop-codon recognition and nascent-polypeptide release from ribosomes during translation. A subsequent complementation test revealed that ESP1 encodes eRF1. We also identified UAA as the stop codon of CysP prolamines with reduced concentration in esp1 mutants. Recognition assays and microarray analysis confirmed that ESP1/eRF1 recognizes UAA/UAG, but not UGA. Our results provide convincing evidence that ESP1/eRF1 participates in the translation termination of CysP prolamines during seed development.

Genetic analysis of cysteine-poor prolamin polypeptides reduced in the endosperm of the rice esp1 mutant

The esp1 mutant CM21 specifically exhibits reduced levels of cysteine-poor (CysP) prolamin bands with pIs of 6.65, 6.95, 7.10, and 7.35 in rice seed. Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis demonstrated that the bands with pIs 6.65, 6.95, and 7.35 are encoded by different structural genes. These results suggest that the Esp1 locus encodes a regulatory factor involved in the synthesis and/or accumulation of CysP prolamin molecules. Isoelectric focusing (IEF) analysis of CysP prolamins in chromosome substitution lines showed that structural genes for bands with pI values of 6.95, 7.10, and 7.35, which are reduced in esp1 mutant lines, are located as a gene cluster in the 44.2 cM region on chromosome 5.

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.

Contiguous genomic DNA sequence comprising the 19-kD zein gene family from maize

A new approach has been undertaken to analyze the sequences and linear organization of the 19-kD zein genes in maize (Zea mays). A high-coverage, large-insert genomic library of the inbred line B73 based on bacterial artificial chromosomes was used to isolate a redundant set of clones containing members of the 19-kD zein gene family, which previously had been estimated to consist of 50 members. The redundant set of clones was used to create bins of overlapping clones that represented five distinct genomic regions. Representative clones containing the entire set of 19-kD zein genes were chosen from each region and sequenced. Seven bacterial artificial chromosome clones yielded 1,160 kb of genomic DNA. Three of them formed a contiguous sequence of 478 kb, the longest contiguous sequenced region of the maize genome. Altogether, these DNA sequences provide the linear organization of 25 19-kD zein genes, one-half the number previously estimated. It is suggested that the difference is because of haplotypes exhibiting different degrees of gene amplification in the zein multigene family. About one-half the genes present in B73 appear to be expressed. Because some active genes have only been duplicated recently, they are so conserved in their sequence that previous cDNA sequence analysis resulted in "unigenes" that were actually derived from different gene copies. This analysis also shows that the 22- and 19-kD zein gene families shared a common ancestor. Although both ancestral genes had the same incremental gene amplification, the 19-kD zein branch exhibited a greater degree of far-distance gene translocations than the 22-kD zein gene family.

Organization and regulation of zein genes in maize endosperm

Zein, the major storage protein of maize endosperm, is constituted by a group of similar polypeptides encoded by a multigene family. The structural genes are located into three main clusters on chromosomes 4, 7 and 10. The rate of accumulation of zein polypeptides is under the control of several positive regulatory loci. The mutant alleles at these loci (O2, O6, O7, F12, De-B30, Mc) reduce more or less drastically the rate of zein deposition. By analysing the interactions among the mutants, epistatic, additive and synergistic effects were observed indicating the existence of multiple pathways controlling zein deposition. Proteins, other than zeins, associated with theO2, O6andF12loci have been identified and characterized.

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.

RFLP mapping of the maize dzr1 locus, which regulates methionine-rich 10 kDa zein accumulation

The dzrl locus in maize posttranscriptionally regulates the accumulation of methionine-rich 10 kDa zein in the endosperm. An allele of this locus present in the inbred line BSSS53, dzrl + BSSS53, conditions several-fold higher accumulation of the 10 kDa zein in comparison with standard inbred lines, leading to enrichment of methionine content in BSSS53 by 30%. In a population segregating for high and low 10 kDa zein, dzr1 + BSSS53 was found tightly to cosegregate with a 22 kDa zein gene cluster, belonging to the Z1C subfamily of alpha-zeins that is located on chromosome 4S. One member of this gene cluster, azs22/6, was estimated to be located less than 0.4 cM from dzr1 + BSSS53, while three other 22 kDa zein genes mapped 3.4 cM away. Restriction fragment length polymorphism (RFLP) mapping of dzr1 was conducted using additional maize DNA markers and orthologous rice DNA markers. One maize marker, php20725, was identified that mapped 1.1 cM from dzr1, proximal to the centromere. Another marker derived from rice, rz329, mapped 6.6 cM distal to dzr1. Pulsed-field gel electrophoresis (PFGE) of the 22 kDa zein cluster showed that probably all copies of the 22 kDa zein genes are present within a 200 kb SalI fragment. The recombination frequency within this cluster was estimated to be 20-fold higher than that predicted for the maize genome.

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.

Histones and histone genes in higher plants: structure and genomic organization

The primary structure of the plant histone genes has been deduced from the comparison of the nucleotide sequences of 23 genes and 14 cDNAs from eight different species. These data confirmed the extreme conservation of histones H3 and H4 in plant and animal kingdoms. Histone H2B is more variable than H2A and the histone H1 is the less conserved histone. Some interesting observations concerning the non-conserved regions of H2A and H2B in their extended C- and N-terminal regions are reported. Only three plant histone genes were found to possess intervening sequences: one H1 gene and two H3.3 like genes. The most striking differences found between the two kingdoms are the absence from plant histone genes of the palindromic structure existing downstream of the animal genes and the fact that plant histone mRNAs are polyadenylated. This suggests that the post-transcriptional regulation of expression of histone genes is different in the two kingdoms. In plants the multiple copies of the histone genes are organized into multigenic families. In the complex genome of maize the multiple copies of the genes are highly dispersed on the genome.

Molecular characterization of two types of 22 kilodalton alpha-zein genes in a gene cluster in maize

Five genes of the alpha-zein subfamily four (SF4) are located in a 56 kb genomic region of the maize inbred line W22. Their nucleotide and deduced amino acid sequences have been determined. The sequences define two types of alpha-zein SF4 genes-type 1 (T1) and type 2 (T2). The single T1 alpha-zein SF4 gene codes for an alpha-zein protein with a M(r) of about 22,000. This is the first alpha-zein SF4 gene sequenced that contains no early in-frame stop codons in its coding sequence. The four T2 alpha-zein SF4 genes in this cluster contain one or two early in-frame stop codons. In addition, our T1 and T2 genes differ markedly in the base sequences of their distal 5' non-translated flanking regions. The nucleotide and the deduced amino acid sequences of these two types of alpha-zein SF4 genes are similar (greater than 90%) to one another and to all known alpha-zein SF4 genes and cDNAs. Of the known W22 alpha-zein SF4 genes, only one in six does not contain an early in-frame stop codon. If the number of alpha-zein SF4 genes is 15-20, then we estimate that only about 4 of the W22 alpha-zein SF4 genes are without in-frame early stop codons.

Subfamilies of histone H3 and H4 genes are located on most, possibly all of the chromosomes in maize

It has been previously shown that in the genome of maize the multiple copies of the histone H3 and H4 multigenic families are organized into eight to ten subfamilies each containing a variable number of copies. Each subfamily is characterized by a specific proximal environment and thus can be revealed by blot-hybridization with its specific 5' probe. Restriction fragment length polymorphism (RFLP) combined with monosomic analysis was used to localize several H3 and H4 subfamilies on maize chromosomes. H3 and H4 genes were found to be located on most, possibly all of the chromosomes, revealing a remarkably dispersed organization of these multigenic families.

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)

Highly clustered zein gene sequences reveal evolutionary history of the multigene family

We have determined the nucleotide sequences of zein cDNA clones ZG14, ZG15, and ZG35. The three clones have 95 to 98% homology to the previously published sequence of clone A20, and 84% homology to sequences of the zein subfamily A30. Comparison of all sequences of the A30 and A20 subfamilies highlights the following features: the 5' nontranslated regions are 68 and 57 nucleotides in length for the A20- and A30-like mRNAs, respectively, and contain at least three repeats of the consensus sequence ACGAACAAta/gG; the majority of these genes are highly clustered as judged from pulsed-field gel electrophoresis of high molecular weight maize DNA. Furthermore, we discuss a model for the evolution of the multigene family which stresses the special importance of unequal crossingover and gene conversion in this system.

Linkages among zein genes determined by isoelectric focusing

Genetic control of the major zein polypeptides in maize (Zea mays L.) was studied by isoelectric focusing (IEF) in agarose. Linkage relationships were determined by making a number of crosses, then determining the expression of zein polypeptides in backcross seeds. Chromosome linkages were determined by using the markers sugary-1 (for chromosome 4), yellow-8, and a waxy 7-9 translocation (for chromosome 7). Nine zeins were in one linkage group on chromosome 4, six in another linkage group on chromosome 4, and four zeins were in one linkage group on chromosome 7. Some IEF single bands consisted of at least two polypeptides, which were detected by subsequent sodium dodecyl sulfate polyacrylamide gel electrophoresis, by aberrant ratios in backcrosses, or by differing recombination percentages. One zein occurred only in homozygous sugary-1 seeds. Three sets of closely-linked zeins were noted that occurred together almost exclusively in certain inbreds.

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.

Localization of zein genes in maize

The band patterns of zein polypeptides were determined for many commercial inbred corn lines and maize stocks using isofocusing in agarose gels and sodium dodecyl sulfate (SDS)-urea gels. Each inbred line or homozygous maize strain genotype has a distinct zein profile which has been catalogued according to the distance of charge migration and molecular weight (kilodaltons). Several zein polypeptides were mapped to chromosomes 4 and 10 with the use of reciprocal translocations. The mapping of at least two polypeptides on distal 4L and 10L had not been previously reported. The general methods used in the present research will permit the mapping of all the zein polypeptides to chromosomal sites.

Mapping of zein polypeptides after isoelectric focusing on agarose gels

Isoelectric focusing of zein in agarose gels gives sharp separations of at least 25 bands noted among 25 corn-belt inbreds. Six inbreds provided standard bands which were used to construct a pattern map. A method is provided for comparing bands, identified by distance from the cathode, which differ only slightly in position. The 25 inbreds were separated into five groups on the basis of pattern similarity. Some groups contained inbreds derived from widely different sources. Zein isoelectric focusing in agarose should be useful for genotype identification and for determination of varietal purity.

Mucronate, Mc, a dominant gene of maize which interacts with opaque-2 to suppress zein synthesis

This paper describes a new dominant mutation of maize, Mc, which interferes in the endosperm with the synthesis of storage proteins. The mutant is characterized by an opaque phenotype; it reduces the deposition of zein and it increases the level of methionine. The mutation is specifically related to storage protein synthesis since soluble and insoluble carbohydrates are present at normal levels. The main interest of this mutant lies in its synergistic interaction with opaque-2 in repressing zein synthesis. In the double mutant o2Mc the accumulation of zein is reduced to less than 10% of that of the normal endosperm. The control on zein synthesis exerted by the double mutant is at the level of production or stability of translatable zein mRNAs. The double mutant o2Mc germinates well offering the opportunity of using it in biochemical and molecular studies related to storage protein synthesis; the reduced endosperm weight of o2Mc negates its practical utilization in breeding maize for quality.