Molecular analysis of opaque-2 alleles from Zea mays L. reveals the nature of mutational events and the presence of a hypervariable region in the 5' part of the gene

The Italian Research on the Molecular Characterization of Maize Kernel Development

The study of the genetic control of maize seed development and seed-related pathways has been one of the most important themes approached by the Italian scientific community. Maize has always attracted the interest of the Italian community of agricultural genetics since its beginning, as some of its founders based their research projects on and developed their "schools" by adopting maize as a reference species. Some of them spent periods in the United States, where maize was already becoming a model system, to receive their training. In this manuscript we illustrate the research work carried out in Italy by different groups that studied maize kernels and underline their contributions in elucidating fundamental aspects of caryopsis development through the characterization of maize mutants. Since the 1980s, most of the research projects aimed at the comprehension of the genetic control of seed development and the regulation of storage products' biosyntheses and accumulation, and have been based on forward genetics approaches. We also document that for some decades, Italian groups, mainly based in Northern Italy, have contributed to improve the knowledge of maize genomics, and were both fundamental for further international studies focused on the correct differentiation and patterning of maize kernel compartments and strongly contributed to recent advances in maize research.

Kernel lysine content does not increase in some maize opaque2 mutants

The recessive mutant allele of the opaque2 gene (o2) alters the endosperm protein pattern and increases the kernel lysine content of maize (Zea mays L.). In this study, sequencing results showed that the o2 mutant was successfully introgressed into 12 elite normal maize inbred lines by marker assisted selection (MAS). The average genetic similarity between these normal inbred lines and their o2 near-isogenic lines (NILs) was more than 95%. Kernel lysine content increased significantly in most of o2 NILs lines relative to normal elite inbreds, but remained unchanged in the genetic backgrounds Dan598o2 and Liao2345o2. Moreover, the kernel characteristics of these two o2 NILs did not differ from the other inbred lines. The results of lysine content analysis in the F1 hybrids between Liao2345o2 and Dan598o2 and other o2 NILs demonstrated that gene(s) other than opaque2 may control kernel lysine content in these two o2 NILs. The results of zein analysis showed that 22-kD α-zein synthesis was reduced or absent, and the 19-kD α-zein synthesis was greatly reduced compared with the recurrent parents in most o2 NILs except for Dan598o2 and Liao2345o2. Our results indicate that gene(s) other than opaque2 may play more important roles in zein synthesis and kernel lysine content in some maize genetic backgrounds.

The Zea mays mutants opaque-2 and opaque-7 disclose extensive changes in endosperm metabolism as revealed by protein, amino acid, and transcriptome-wide analyses

Background

The changes in storage reserve accumulation during maize (Zea mays L.) grain maturation are well established. However, the key molecular determinants controlling carbon flux to the grain and the partitioning of carbon to starch and protein are more elusive. The Opaque-2 (O2) gene, one of the best-characterized plant transcription factors, is a good example of the integration of carbohydrate, amino acid and storage protein metabolisms in maize endosperm development. Evidence also indicates that the Opaque-7 (O7) gene plays a role in affecting endosperm metabolism. The focus of this study was to assess the changes induced by the o2 and o7 mutations on maize endosperm metabolism by evaluating protein and amino acid composition and by transcriptome profiling, in order to investigate the functional interplay between these two genes in single and double mutants.

Results

We show that the overall amino acid composition of the mutants analyzed appeared similar. Each mutant had a high Lys and reduced Glx and Leu content with respect to wild type. Gene expression profiling, based on a unigene set composed of 7,250 ESTs, allowed us to identify a series of mutant-related down (17.1%) and up-regulated (3.2%) transcripts. Several differentially expressed ESTs homologous to genes encoding enzymes involved in amino acid synthesis, carbon metabolism (TCA cycle and glycolysis), in storage protein and starch metabolism, in gene transcription and translation processes, in signal transduction, and in protein, fatty acid, and lipid synthesis were identified. Our analyses demonstrate that the mutants investigated are pleiotropic and play a critical role in several endosperm-related metabolic processes. Pleiotropic effects were less evident in the o7 mutant, but severe in the o2 and o2o7 backgrounds, with large changes in gene expression patterns, affecting a broad range of kernel-expressed genes.

Conclusion

Although, by necessity, this paper is descriptive and more work is required to define gene functions and dissect the complex regulation of gene expression, the genes isolated and characterized to date give us an intriguing insight into the mechanisms underlying endosperm metabolism.

Chromatin and DNA modifications in the Opaque2-mediated regulation of gene transcription during maize endosperm development

The maize (Zea mays) Opaque2 (O2) gene encodes an endosperm-specific bZIP-type transcription activator. In this study, we analyzed O2 targets for chromatin and DNA modifications and transcription factors binding during endosperm development and in leaves. In leaves, O2 targets exhibit high cytosine methylation levels and transcriptionally silent chromatin, enriched with histones H3 dimethylated at Lys-9 (H3K9me2) and Lys-27 (H3K27me2). Transcriptional activation in the endosperm occurs through a two-step process, with an early potentiated state and a later activated state. The potentiated state has cytosine demethylation at symmetric sites, substitution of H3K9me2 and H3K27me2 with histones H3 acetylated at Lys-14 (H3K14ac) and dimethylated at Lys-4 (H3K4me2), and increased DNaseI sensitivity. During the activated state, the mRNA of O2 targets accumulates in correspondence to RNPII, O2, and Ada2/Gcn5 coactivator binding. The active state also exhibits further increases of H3K14ac/H3K4me2 and DNaseI accessibility levels and deposition of histone H3 acetylated at Lys-9 and trimethylated at Lys-4. Analysis of o2 mutants revealed that O2 targets differ in their dependence on O2 activity for coactivator recruitment and for formation of specific chromatin modification profiles. These results indicate gene-specific involvement of mechanisms that modify chromatin states in the O2-mediated regulation of transcription.

Colocation between a gene encoding the bZip factor SPA and an eQTL for a high-molecular-weight glutenin subunit in wheat (Triticum aestivum)

The quality of wheat grain is largely determined by the quantity and composition of storage proteins (prolamins) and depends on mechanisms underlying the regulation of expression of prolamin genes. The endosperm-specific wheat basic region leucine zipper (bZIP) factor storage protein activator (SPA) is a positive regulator that binds to the promoter of a prolamin gene. The aim of this study was to map SPA (the gene encoding bZIP factor SPA) and genomic regions associated with quantitative variations of storage protein fractions using F7 recombinant inbred lines (RILs) derived from a cross between Triticum aestivum "Renan" and T. aestivum "Récital". SPA was mapped through RFLP using a cDNA probe and a specific single nucleotide polymorphism (SNP) marker. Storage protein fractions in the parents and RILs were quantified using capillary electrophoresis. Quantitative trait loci (QTLs) for protein were detected and mapped on six chromosome regions. One QTL, located on the long arm of chromosome 1B, explained 70% of the variation in quantity of the x subunit of Glu-B1. Genetic mapping suggested that SPA is located on chromosome arm 1L and is also present in the confidence interval of the corresponding QTL for Glu-B1x on 1BL, suggesting that SPA might be a candidate gene for this QTL.

Analysis of the methylation pattern of the maize opaque-2 (O2) promoter and in vitro binding studies indicate that the O2 B-Zip protein and other endosperm factors can bind to methylated target sequences

The maize opaque-2 locus (o2) has an endosperm-specific expression and is positively autoregulated by its gene product, a b-Zip protein, to a TGACGTTG motif. The genomic sequencing method was used here to describe, in leaf and endosperm, the methylation pattern of a 390-base pair region of the o2 promoter. In leaf, 96% of the C residues are methylated, whereas in endosperm the 5-methylcytosine content is 84%. Comparison of these methylation patterns indicates that the o2 tissue-specific expression does not result from the demethylation of any specific C residue and that, in vivo, O2 interacts with a methylated target sequence. Consistently, gel-shift experiments using a CpG-methylated, partially methylated, and hemimethylated o2 promoter fragments showed that, in vitro, the O2 protein binds to the major groove of a methylated target sequence, although its binding activity decreases at increasing levels of C-methylation and is more effectively reduced by methylation of the lower strand than of the upper strand of the DNA. Using partially purified endosperm cell extracts, we also show that, besides the O2 protein, other proteins specifically bind to a partially methylated o2 promoter fragment, therefore indicating that in plants a subset of different proteins may mediate the expression of a naturally occurring methylated o2 promoter.

The transcriptional activator Opaque-2 controls the expression of a cytosolic form of pyruvate orthophosphate dikinase-1 in maize endosperms

The maize Opaque-2 (O2) protein is a transcription factor of the basic/leucine-zipper class, involved in the regulation of endosperm proteins including the 22kDa alpha-zein storage proteins and b32 protein. In this study we have focussed our attention on the relationship between O2 and the cyPPDK1 gene, which encodes a cytoplasmic pyruvate orthophosphate dikinase (PPDK) isoform. The results of this study showed that PPDK activity is detectable in wild-type maize endosperms, while in o2 mutant endosperms, the levels of PPDK protein, mRNA and enzymatic activity are reduced, indicating that O2 is involved in the regulation of cyPPDK1 in this tissue. By employing transient expression experiments in tobacco mesophyll protoplasts, we have demonstrated that the O2 protein can activate expression of a chloramphenicol acetyl transferase reporter gene placed under the control of the cyPPDK1 promoter. An in vitro binding assay and DNaseI footprint analysis demonstrated that a specific sequence in the cyPPDK1 promoter can be recognized and protected by maize O2 protein. The regulation by the O2 locus of cyPPDK1 reported here, and control of alpha-zein synthesis by O2 suggest that the O2 protein may play a more general role in maize endosperm development than previously thought.