Recent proliferation and translocation of pollen group 1 allergen genes in the maize genome

Gametophyte genome activation occurs at pollen mitosis I in maize

Flowering plants alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. Pollen actively transcribes its haploid genome, providing phenotypic diversity even among pollen grains from a single plant. In this study, we used allele-specific RNA sequencing of single pollen precursors to follow the shift to haploid expression in maize pollen. We observed widespread biallelic expression for 11 days after meiosis, indicating that transcripts synthesized by the diploid sporophyte persist long into the haploid phase. Subsequently, there was a rapid and global conversion to monoallelic expression at pollen mitosis I, driven by active new transcription from the haploid genome. Genes showed evidence of increased purifying selection if they were expressed after (but not before) pollen mitosis I. This work establishes the timing during which haploid selection may act in pollen.

Immunoinformatic epitope prediction to select monoclonal antibodies for Phl p 1 quantification

BACKGROUND

Allergen quantification has become a relevant parameter for allergen extract characterization and to guarantee the consistency of the manufacturing process at allergen immunotherapy. The aim of this study was to develop and validate a method to quantify the major allergen Phl p 1 based on a prediction of the antigenic regions by immunoinformatic strategies.

METHODS

Phl p 1 was purified from a Phleum pratense native extract by chromatographic methods. Immunoinformatic tools were used to predict B-cell epitopes. In silico predictions were verified by mapping linear epitopes with a peptide library and used to select the appropriate regions for producing the mAbs to develop an ELISA method, which was validated. Phl p 1 was quantified in 24 batches of P. pratense extracts.

RESULTS

Phl p 1 was purified with 95 % purity and completely functional. Eight B-cell epitopes in each of the two Phl p 1 isoforms were predicted. Two of the predicted B-cell epitopes overlapped with the experimentally determined peptides recognized by two mAbs selected for development of the kit. The quantification method demonstrated to be specific to Phl p 1, linear, accurate and precise in the range from 7.7 to 123.3 μg/mg. Mean Phl p 1 content was 28.95 μg of allergen/mg of lyophilized native extract and 44.23 μg of allergen/mg of lyophilized depigmented extract.

CONCLUSIONS

An ELISA method for measuring Phl p 1 in P. pratense extracts was developed and validated by producing the appropriate mAbs against epitopes selected by immunoinformatic tools.

Two Expansin Genes, AtEXPA4 and AtEXPB5, Are Redundantly Required for Pollen Tube Growth and AtEXPA4 Is Involved in Primary Root Elongation in Arabidopsis thaliana

The growth of plant cells is inseparable from relaxation and expansion of cell walls. Expansins are a class of cell wall binding proteins, which play important roles in the relaxation of cell walls. Although there are many members in expansin gene family, the functions of most expansin genes in plant growth and development are still poorly understood. In this study, the functions of two expansin genes, AtEXPA4 and AtEXPB5 were characterized in Arabidopsis thaliana. AtEXPA4 and AtEXPB5 displayed consistent expression patterns in mature pollen grains and pollen tubes, but AtEXPA4 also showed a high expression level in primary roots. Two single mutants, atexpa4 and atexpb5, showed normal reproductive development, whereas atexpa4atexpb5 double mutant was defective in pollen tube growth. Moreover, AtEXPA4 overexpression enhanced primary root elongation, on the contrary, knocking out AtEXPA4 made the growth of primary root slower. Our results indicated that AtEXPA4 and AtEXPB5 were redundantly involved in pollen tube growth and AtEXPA4 was required for primary root elongation.

Genome-wide identification, characterization, and expression analysis of the expansin gene family in watermelon (Citrullus lanatus)

Expansins are plant cell-wall loosening proteins involved in cell enlargement, adaptive responses to environmental stimuli, and various developmental processes. Although expansins have been characterized in many plant species, little is reported on this family in watermelon. In this study, 30 expansin genes in the watermelon genome (ClEXPs) were identified. These genes which were divided into four subfamilies (7 ClEXLAs, 2 ClEXLBs, 18 ClEXPAs, and 3 ClEXPBs) are unevenly distribute on 10 of 11 watermelon chromosomes. Chromosome mapping suggested that tandem duplication events may have played important roles in the expanding of watermelon expansins. Gene structure and motif identification revealed that same subfamily and subgroup have conserved gene structure and motif. Detection of cis-acting elements revealed that ClEXPs gene promoter regions were enriched with light-responsive elements, hormone-responsive, environmental stress-related, and development-related elements. Expression patterns of ClEXPs were investigated by qRT-PCR. The results showed that expression patterns of 15 ClEXP genes differed in three tissues. Through our own and public RNA-seq analysis, we found that ClEXPs had different expression patterns in fruit flesh, fruit rind, and seed at various developmental stages, and most of ClEXPs were highly responsive to abiotic and biotic stresses. Remarkably, 7 ClEXPs (ClEXLA1, ClEXLA6, ClEXLB1, ClEXLB2, ClEXPA5, ClEXPA10, and ClEXPA16) exhibited positive response to at least three kinds of stresses, suggesting that they might play important roles in the crosstalk of stress signal pathways. The results of this study provide useful insights for the functional identification of expansin gene family in watermelon.

High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2. Overall, our study demonstrates a developmentally programmed and coordinated transcriptional activation of TEs and genes in pollen, and further identifies maize pollen as a model in which transcriptomic data have predictive value for quantitative phenotypes.

Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.)

Main conclusion 30 expansin genes were identified in the jujube genome. Phylogenetic analysis classified expansins into 17 subgroups. Closely related expansins share a conserved gene structure. ZjEXPs had different expression patterns in different tissues. Plant-specific expansins were first discovered as pH-dependent cell-wall-loosening proteins involved in diverse physiological processes. No comprehensive analysis of the expansin gene family has yet been carried out at the whole genome level in Chinese jujube (Ziziphus jujuba Mill.). In this study, 30 expansin genes were identified in the jujube genome. These genes, which were distributed with varying densities across 10 of the 12 jujube chromosomes, could be divided into four subfamilies: 19 ZjEXPAs, 3 ZjEXPBs, 1 ZjEXLA, and 7 ZjEXLBs. Phylogenetic analysis of expansin genes in Arabidopsis, rice, apple, grape, and jujube classified these genes into 17 subgroups. Members of the same subfamily and subgroup shared conserved gene structure and motif compositions. Homology analysis identified 20 homologous gene pairs between jujube and Arabidopsis. Further analysis of ZjEXP gene promoter regions uncovered various growth, development and stress-responsive cis-acting elements. Expression analysis and transcript profiling revealed that ZjEXPs had different expression patterns in different tissues at various developmental stages. ZjEXPA4 and ZjEXPA6 were highly expressed in young fruits, ZjEXPA3 and ZjEXPA5 were significantly expressed in flowers, and ZjEXPA7 was specifically expressed in young leaves. The results of this study, the first systematic analysis of the jujube expansin gene family, can serve as a strong foundation for further elucidation of the physiological functions and biological roles of jujube expansin genes.

Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System

Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional characterization in related grass species.

The Pollen Coat Proteome: At the Cutting Edge of Plant Reproduction

The tapetum is a single layer of secretory cells which encloses the anther locule and sustains pollen development and maturation. Upon apoptosis, the remnants of the tapetal cells, consisting mostly of lipids and proteins, fill the pits of the sculpted exine to form the bulk of the pollen coat. This extracellular matrix forms an impermeable barrier that protects the male gametophyte from water loss and UV light. It also aids pollen adhesion and hydration and retains small signaling compounds involved in pollen-stigma communication. In this study, we have updated the list of the pollen coat's protein components and also discussed their functions in the context of sexual reproduction.

Evolutionary divergence of β-expansin structure and function in grasses parallels emergence of distinctive primary cell wall traits

Expansins are wall-loosening proteins that promote the extension of primary cell walls without the hydrolysis of major structural components. Previously, proteins from the EXPA (α-expansin) family were found to loosen eudicot cell walls but to be less effective on grass cell walls, whereas the reverse pattern was found for EXPB (β-expansin) proteins obtained from grass pollen. To understand the evolutionary and structural bases for the selectivity of EXPB action, we assessed the extension (creep) response of cell walls from diverse monocot families to EXPA and EXPB treatments. Cell walls from Cyperaceae and Juncaceae (families closely related to grasses) displayed a typical grass response ('β-response'). Walls from more distant monocots, including some species that share with grasses high levels of arabinoxylan, responded preferentially to α-expansins ('α-response'), behaving in this regard like eudicots. An expansin with selective activity for grass cell walls was detected in Cyperaceae pollen, coinciding with the expression of genes from the divergent EXPB-I branch that includes grass pollen β-expansins. The evolutionary origin of this branch was located within Poales on the basis of phylogenetic analyses and its association with the 'sigma' whole-genome duplication. Accelerated evolution in this branch has remodeled the protein surface in contact with the substrate, potentially for binding highly substituted arabinoxylan. We propose that the evolution of the divergent EXPB-I group made a fundamental change in the target and mechanism of wall loosening in the grass lineage possible, involving a new structural role for xylans and the expansins that target them.

A genome-wide analysis of the expansin genes in Malus × Domestica

Expansins were first identified as cell wall-loosening proteins; they are involved in regulating cell expansion, fruits softening and many other physiological processes. However, our knowledge about the expansin family members and their evolutionary relationships in fruit trees, such as apple, is limited. In this study, we identified 41 members of the expansin gene family in the genome of apple (Malus × Domestica L. Borkh). Phylogenetic analysis revealed that expansin genes in apple could be divided into four subfamilies according to their gene structures and protein motifs. By phylogenetic analysis of the expansins in five plants (Arabidopsis, rice, poplar, grape and apple), the expansins were divided into 17 subgroups. Our gene duplication analysis revealed that whole-genome and chromosomal-segment duplications contributed to the expansion of Mdexpansins. The microarray and expressed sequence tag (EST) data showed that 34 Mdexpansin genes could be divided into five groups by the EST analysis; they may also play different roles during fruit development. An expression model for MdEXPA16 and MdEXPA20 showed their potential role in developing fruit. Overall, our study provides useful data and novel insights into the functions and regulatory mechanisms of the expansin genes in apple, as well as their evolution and divergence. As the first step towards genome-wide analysis of the expansin genes in apple, our results have established a solid foundation for future studies on the function of the expansin genes in fruit development.

Matrix solubilization and cell wall weakening by β-expansin (group-1 allergen) from maize pollen

Beta-expansins accumulate to high levels in grass pollen, a feature apparently unique to grasses. These proteins, which are major human allergens, facilitate pollen tube penetration of the maize stigma and style (the silk). Here we report that treatment of maize silk cell walls with purified β-expansin from maize pollen led to solubilization of wall matrix polysaccharides, dominated by feruloyated highly substituted glucuronoarabinoxylan (60%) and homogalacturonan (35%). Such action was selective for cell walls of grasses, and indicated a target preferentially found in grass cell walls, probably the highly substituted glucuronoarabinoxylan. Several tests for lytic activities by β-expansin were negative and polysaccharide solubilization had weak temperature dependence, which indicated a non-enzymatic process. Concomitant with matrix solubilization, β-expansin treatment induced creep, reduced the breaking force and increased the plastic compliance of wall specimens. From comparisons of the pH dependencies of these processes, we conclude that matrix solubilization was linked closely to changes in wall plasticity and breaking force, but not so closely coupled to cell wall creep. Because matrix solubilization and increased wall plasticity have not been found with other expansins, we infer that these novel activities are linked to the specialized role of grass pollen β-expansins in promotion of penetration of the pollen tube through the stigma and style, most likely by weakening the middle lamella.

Structure-function analysis of the bacterial expansin EXLX1

We made use of EXLX1, an expansin from Bacillus subtilis, to investigate protein features essential for its plant cell wall binding and wall loosening activities. We found that the two expansin domains, D1 and D2, need to be linked for wall extension activity and that D2 mediates EXLX1 binding to whole cell walls and to cellulose via distinct residues on the D2 surface. Binding to cellulose is mediated by three aromatic residues arranged linearly on the putative binding surface that spans D1 and D2. Mutation of these three residues to alanine eliminated cellulose binding and concomitantly eliminated wall loosening activity measured either by cell wall extension or by weakening of filter paper but hardly affected binding to whole cell walls, which is mediated by basic residues located on other D2 surfaces. Mutation of these basic residues to glutamine reduced cell wall binding but not wall loosening activities. We propose domain D2 as the founding member of a new carbohydrate binding module family, CBM63, but its function in expansin activity apparently goes beyond simply anchoring D1 to the wall. Several polar residues on the putative binding surface of domain D1 are also important for activity, most notably Asp82, whose mutation to alanine or asparagine completely eliminated wall loosening activity. The functional insights based on this bacterial expansin may be extrapolated to the interactions of plant expansins with cell walls.

Genetic resources for maize cell wall biology

Grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression profiles, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript profile data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-specific genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of field-grown lines by near-infrared spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis-molecular beam mass spectrometry confirmed that several nir mutants had altered carbohydrate-lignin compositions.

Class B beta-expansins are needed for pollen separation and stigma penetration

Group 1 grass pollen allergens comprise a distinctive clade within the beta-expansin family of cell wall-loosening proteins and are divided by sequence divergence into two phylogenetically separable classes (A and B). They have been proposed to loosen the walls of the stigma and style. Supporting this idea, we recently showed that a transposon insertion in one of the maize group-1 allergen genes reduces the ability of pollen to effect fertilization under conditions of pollen competition. In this work, we provide additional information on the phenotype of this mutant, showing that pollen deficient in beta-expansin gene expression tended to form large aggregates, leading to poor pollen dispersal on anther dehiscence, and that emerging pollen tubes had difficulties entering the silk. In addition, a silencing construct was created to reduce expression of all the class B genes with results that are consistent with those seen with the transposon insertional line, including reduced transgene transmission through the pollen. Our results provide a more detailed understanding of the role of group 1 allergens (pollen beta-expansins) in maize pollen development, pollen dispersal, pollen tube penetration into the style, and pollen tube growth through the transmitting tract.

Transcriptome-based examination of putative pollen allergens of rice (Oryza sativa ssp. japonica)

Pollen allergens are among the most abundantly transcribed and translated products in the life history of plants, and particularly grasses. To identify different pollen allergens in rice, putative allergens were identified in the rice genome and their expression characterized using the Affymetrix 57K rice GeneChip microarray. Among the most abundant pollen-specific candidate transcripts were Ory s 1 beta-expansin, Ory s 2, Ory s 7 EF hand, Ory s 11, Ory s 12 profilin A, Ory s 23, glycosyl hydrolase family 28 (polygalacturonase), and FAD binding proteins. Highly expressed pollen proteins are frequently present in multiple copy numbers, sometimes with mirror images located on nearby regions of the opposite DNA strand. Many of these are intronless and inserted as copies that retain nearly exact copies of their regulatory elements. Ory s 23 reflects low variability and high copy number, suggesting recent gene amplification. Some copies contain pseudogenes, which may reflect their origin through activity of retrotransposition; some putative allergenic sequences bear fusion products with repeat sequences of transposable elements (LTRs). The abundance of nearby repetitive sequences, activation of transposable elements, and high production of mRNA transcripts appear to coincide in pollen and may contribute to a syndrome in which highly transcribed proteins may be copied and inserted with streamlined features for translation, including grouping and removal of introns.

Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development

To study the correlation of the sequence positions on the physical DNA finger print contig (FPC) map and cytogenetic maps of pachytene and somatic maize chromosomes, sequences located along the chromosome 9 FPC map approximately every 10 Mb were selected to place on maize chromosomes using fluorescent in situ hybridization (FISH). The probes were produced as pooled polymerase chain reaction products based on sequences of genetic markers or repeat-free portions of mapped bacterial artificial chromosome (BAC) clones. Fifteen probes were visualized on chromosome 9. The cytological positions of most sequences correspond on the pachytene, somatic, and FPC maps except some probes at the pericentromeric regions. Because of unequal condensation of mitotic metaphase chromosomes, being lower at pericentromeric regions and higher in the arms, probe positions are displaced to the distal ends of both arms. The axial resolution of FISH on somatic chromosome 9 varied from 3.3 to 8.2 Mb, which is 12-30 times lower than on pachytene chromosomes. The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements.

Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes

Combined with a system for identifying each of the chromosomes in a genome, visualizing the location of individual genetic loci by fluorescence in situ hybridization (FISH) would aid in assembling physical and genetic maps. Previously, large genomic clones have been successfully used as FISH probes onto somatic chromosomes but this approach is complicated in species with abundant repetitive elements. In this study, repeat-free portions of sequences that were anchored to particular chromosomes including genes, gene clusters, large cDNAs, and portions of BACs obtained from public databases were used to label the corresponding physical location using FISH. A collection of probes that includes at least one marker on each chromosome in the maize complement was assembled, allowing a small-target karyotyping system to be developed. This set provides the foundation onto which additional loci could be added to strengthen further the ability to perform chromosomal identification in maize and its relatives. The probes were demonstrated to produce signals in several wild relatives of maize, including Zea luxurians, Z. diploperennis, and Tripsacum dactyloides.