Genome-Wide Analysis of the Expansin Gene Superfamily Reveals Grapevine-Specific Structural and Functional Characteristics

Background

Expansins are proteins that loosen plant cell walls in a pH-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. The expansin superfamily (EXP) comprises four distinct families: expansin A (EXPA), expansin B (EXPB), expansin-like A (EXLA) and expansin-like B (EXLB). There is experimental evidence that EXPA and EXPB proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact functions of EXLA and EXLB remain unclear. The complete grapevine (Vitis vinifera) genome sequence has allowed the characterization of many gene families, but an exhaustive genome-wide analysis of expansin gene expression has not been attempted thus far.

Methodology/Principal Findings

We identified 29 EXP superfamily genes in the grapevine genome, representing all four EXP families. Members of the same EXP family shared the same exon–intron structure, and phylogenetic analysis confirmed a closer relationship between EXP genes from woody species, i.e. grapevine and poplar (Populus trichocarpa), compared to those from Arabidopsis thaliana and rice (Oryza sativa). We also identified grapevine-specific duplication events involving the EXLB family. Global gene expression analysis confirmed a strong correlation among EXP genes expressed in mature and green/vegetative samples, respectively, as reported for other gene families in the recently-published grapevine gene expression atlas. We also observed the specific co-expression of EXLB genes in woody organs, and the involvement of certain grapevine EXP genes in berry development and post-harvest withering.

Conclusion

Our comprehensive analysis of the grapevine EXP superfamily confirmed and extended current knowledge about the structural and functional characteristics of this gene family, and also identified properties that are currently unique to grapevine expansin genes. Our data provide a model for the functional characterization of grapevine gene families by combining phylogenetic analysis with global gene expression profiling.     

Regulation of Histone Methylation and Reprogramming of Gene Expression in the Rice Inflorescence Meristem

Rice inflorescence meristem (IM) activity is essential for panicle development and grain production. How chromatin and epigenetic mechanisms regulate IM activity remains unclear. Genome-wide analysis revealed that in addition to genes involved in the vegetative to reproductive transition, many metabolic and protein synthetic genes were activated in IM compared with shoot apical meristem and that a change in the H3K27me3/H3K4me3 ratio was an important factor for the differential expression of many genes. Thousands of genes gained or lost H3K27me3 in IM, and downregulation of the H3K27 methyltransferase gene SET DOMAIN GROUP 711 (SDG711) or mutation of the H3K4 demethylase gene JMJ703 eliminated the increase of H3K27me3 in many genes. SDG711-mediated H3K27me3 repressed several important genes involved in IM activity and many genes that are silent in the IM but activated during floral organogenesis or other developmental stages. SDG711 overexpression augmented IM activity and increased panicle size; suppression of SDG711 by RNA interference had the opposite effect. Double knockdown/knockout of SDG711 and JMJ703 further reduced panicle size. These results suggest that SDG711 and JMJ703 have agonistic functions in reprogramming the H3K27me3/H3K4me3 ratio and modulating gene expression in the IM.     

Structural and functional characteristics of photosynthetic apparatus of chlorophyll-containing grape vine tissue

Photosynthesis in tissues under periderm of woody stems and shoots of perennial plants occurs in environment that is very different from the internal environment of leaf chloroplasts. These tissues are characterized by high CO₂ and low O₂ concentrations, more acidic surroundings, besides that only light which have passed through periderm reaches photosynthetic antennas. In contrast to leaves of deciduous plants chlorenchyma tissues of wintering plant organs are exposed to temperature fluctuations during all seasons, that is why the photosynthetic apparatus of woody stems has to be able to adapt to a wide range of environmental temperatures. In order to reveal unique features, which enable photosynthetic apparatus of chlorenchyma cells in woody plant organs to implement biological functions under different light and temperature conditions, we studied photosynthetic tissues of stem cortex in grapevine (Vitis vinifera L.) under normal conditions and after exposure to suboptimal temperatures and high light intensity. Comparative analysis of photosynthetic pigment composition and low-temperature chlorophyll fluorescence emission spectrum of leaves, young shoots and chlorenchyma of lignified shoots revealed relatively high level of chlorophyll b and carotenoids, and high photosystem II (PSII) to photosystem I (PSI) ratio in woody shoots. Analysis of parameters of variable chlorophyll fluorescence revealed high PSII activity in grapevine shoot cortex and demonstrated improved freeze tolerance and higher sensitivity to light of photosynthetic apparatus in grape vine in comparison to leaves. It was shown for the first time that photosynthetic apparatus in chlorenchyma cells of vine undergoes so-called “state-transition”–fast rearrangements leading to redistribution of energy between photosystems. Analysis of fatty acid (FA) compositions of lipids in examined tissues showed that the FA unsaturation index in green tissue of vine is lower than in leaves. A distinct feature of FA compositions of lipids in vine cortex was relatively high level of linoleic acid.     

Red young leaves have less mechanical defence than green young leaves

In many plants, leaves that are young and/or old (senescent) are not green. One adaptive hypothesis proposed that leaf color change could be a warning signal reducing insect attack. If leaf coloration involves less herbivory, it remains unclear why leaves in many species are constantly green. To examine whether green leaves reduce herbivory by physical defense as an alternative to the supposed warning signal of red leaves, we conducted comparative analyses of leaf color and protective tissues of 76 woody species in spring. The protective features (trichomes, enhanced cuticle and multiple epidermis) and the distribution of red pigments within leaves were examined in both young and mature leaves. We observed that redness was more frequent in young leaves than in senescent leaves. Compared to 36 species with red young leaves, 40 species with green young leaves showed a significantly higher incidence of enhanced cuticle and trichomes in both phylogenetic and non‐phylogenetic analyses. The phylogenetic analysis indicated that the multiple origins of mechanical protection were generally associated with loss of red coloration. Our finding of relatively poor mechanical protection in red young leaves provides additional evidence for the adaptive explanation of leaf color change.     

Pigment dynamics and autumn leaf senescence in a New England deciduous forest,eastern USA

The leaves of woody plants at Harvard Forest in Central Massachusetts, USA, changed color during senescence; 70% (62/89) of the woody species examined anatomically contained anthocyanins during senescence. Anthocyanins were not present in summer green leaves, and appeared primarily in the vacuoles of palisade parenchyma cells. Yellow coloration was a result of the unmasking of xanthophyll pigments in senescing chloroplasts. In nine red-senescing species, anthocyanins were not detectable in mature leaves, and were synthesized de novo in senescence, with less than 20µg cm^–2 of chlorophyll remaining. Xanthophyll concentrations declined in relation to chlorophyll to the same extent in both yellow- and red-leaved taxa. Declines in the maximum photosystemII quantum yield of leaves collected prior to dawn were only slightly less in the red-senescing species, indicating no long-term protective activity. Red-leaved species had significantly greater mass/area and lower chlorophylla/b ratios during senescence. Nitrogen tissue concentrations in mature and senescent leaves negatively correlated to anthocyanin concentrations in senescent leaves, weak evidence for more efficient nitrogen resorption in anthocyanic species. Shading retarded both chlorophyll loss and anthocyanin production in Cornus alternifolia, Acer rubrum, Acer saccharum, Quercus rubra and Viburnum alnifolium. It promoted chlorophyll loss in yellow-senescing Fagus grandifolia. A reduced red:far-red ratio did not affect this process. Anthocyanins did not increase leaf temperatures in Q.rubra and Vaccinium corymbosum on cold and sunny days. The timing of leaf-fall was remarkably constant from year to year, and the order of senescence of individual species was consistent.     

Bionomics of <Emphasis Type="Italic">Momordica cochinchinensis</Emphasis> Fed <Emphasis Type="Italic">Aulacophora foveicollis</Emphasis> (Coleoptera: Chrysomelidae)

The effects of feeding on root by the larvae and three types of Momordica cochinchinensis Spreng (Cucubitaceae) leaves (young, mature and senescent) by the adults of Aulacophora foveicollis Lucas (Coleoptera: Chrysomelidae) were studied under laboratory conditions. Total larval developmental time was 19.7 ± 0.2 days by feeding on young roots. Adult males lived for 28.4 ± 1, 65.7 ± 1.1 and 22.8 ± 1.3 days on young, mature and senescent leaves, respectively; whilst adult females lived for 34.3 ± 1.2, 68.5 ± 0.9 and 26.4 ± 1.4 days on young, mature and senescent leaves, respectively. Fecundity was highest in mature leaves fed insects (202.2 ± 10.6). Total carbohydrate, protein, lipid, nitrogen and amino acid were much higher in root followed by mature leaves than young and senescent leaves. Moisture content was highest in mature leaves than the roots, young and senescent leaves. Phenols were greatest in young leaves followed by mature leaves and least in senescent leaves and roots of the said plant. Flavonols were higher in young leaves and least in root. These results suggest that A. foveicollis adults perform better on mature leaves than young and senescent leaves for their nutrition.     

The Occurence of delta-Tocopherylquinone in Higher Plants and Its Relation to Senescence

delta-Tocopherylquinone (deltaTQ) content was determined in tobacco and yellow maple leaves, green ivy leaves and cactus tissues. It was found that the concentration of delta-TQ was highest in mature or senescent tissues, such as white tobacco leaves (0.02 mumole/g dry wt) while its detection was uncertain in young, green leaves from the apex of tobacco plants. Fractionation by centrifugation of senescent tobacco leaves showed that the osmiophilic globule fraction was enriched in delta-TQ. Electron microscope studies of young, mature and senescent tobacco tissues showed progressive changes in the size and number of osmiophilic globules. After chloroplast breakdown in senescent tobacco leaves, these globules became the predominant constituents of the organelle. delta-TQ which is associated with osmiophilic globules may play a role in the development of plants, particularly during senescence.     

The Occurence of δ-Tocopherylquinone in Higher Plants and Its Relation to Senescence

δ-Tocopherylquinone (δTQ) content was determined in tobacco and yellow maple leaves, green ivy leaves and cactus tissues. It was found that the concentration of δ-TQ was highest in mature or senescent tissues, such as white tobacco leaves (0.02 μmole/g dry wt) while its detection was uncertain in young, green leaves from the apex of tobacco plants. Fractionation by centrifugation of senescent tobacco leaves showed that the osmiophilic globule fraction was enriched in δ-TQ. Electron microscope studies of young, mature and senescent tobacco tissues showed progressive changes in the size and number of osmiophilic globules. After chloroplast breakdown in senescent tobacco leaves, these globules became the predominant constituents of the organelle. δ-TQ which is associated with osmiophilic globules may play a role in the development of plants, particularly during senescence.     

Characterization of a stress-induced,developmentally regulated gene family from soybean

We describe a family of stress-induced, developmentally regulated soybean genes for which cDNAs have been obtained from two different cultivars (Glycine max cv. Mandarin and Glycine max cv. Williams). The mRNAs corresponding to these cDNAs, called SAM22 and H4, respectively, accumulate predominantly in the roots of soybean seedlings but are present at high levels in the roots and leaves of mature plants. SAM22 accumulation is especially dramatic in senescent leaves. In addition, SAM22 accumulation can be induced in young leaves by wounding or by transpiration-mediated uptake of salicylic acid, methyl viologen, fungal elicitor, hydrogen peroxide or sodium phosphate (pH 6.9). Taken together, these data indicate that the genes corresponding to SAM22 and H4 are induced by various stresses and developmental cues. Southern blot analysis indicates that multiple copies of sequences related to SAM22 exist in the soybean genome. We also show that the nucleotide sequences of the cDNAs corresponding to SAM22 and H4 are 86% identical at the nucleotide level to each other and 70% identical at the amino acid level to the disease resistance response proteins of Pisum sativum.     

Ultrastructural aspects of petal development inCucumis sativus with particular reference to the chromoplasts

Summary Changes in fine structure in petals ofCucumis have been followed from an early green stage, through maturity, to a senescent dark yellow stage. The most noticable changes occur in the plastids. In chloroplasts of young green petals bundles of tubules appear in the stroma and increase in number as the thylakoids disappear. The entire plastid is eventually filled by groups of tubules orientated in different planes, separated by a few remaining swollen thylakoids. It is proposed that these chromoplast tubules represent a reorganization of the thylakoid material. In the mature chromoplast these tubules have become widely separated and randomly orientated, the whole plastid being approximately five times the volume of the chloroplast from which it was derived. Chromoplasts in senescent petals show a number of cytoplasmic invaginations.Other cytoplasmic components show degredative changes throughout petal maturation corresponding to the senescence syndrome found in cucumber leaves and cotyledons.The significance of the observations is discussed.One of us (M. S.) acknowledges receipt of a Science Research Council Studentship.