Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes

Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster for genes encoding three families of histone deacetylase (HDAC) proteins and three families of histone acetyltransferase (HAT) proteins. Plants, animals and fungi were found to have a single member of each of three subfamilies of the GNAT family of HATs, suggesting conservation of these functions. However, major differences were found with respect to sizes of gene families and multi-domain protein structures within other families of HATs and HDACs, indicating substantial evolutionary diversification. Phylogenetic analysis identified a new class of HDACs within the RPD3/HDA1 family that is represented only in plants and animals. A similar analysis of the plant-specific HD2 family of HDACs suggests a duplication event early in dicot evolution, followed by further diversification in the lineage leading to Arabidopsis. Of three major classes of SIR2-type HDACs that are found in animals, fungi have representatives only in one class, whereas plants have representatives only in the other two. Plants possess five CREB-binding protein (CBP)-type HATs compared with one to two in animals and none in fungi. Domain and phylogenetic analyses of the CBP family proteins showed that this family has evolved three distinct types of CBPs in plants. The domain architecture of CBP and TAF(II)250 families of HATs show significant differences between plants and animals, most notably with respect to bromodomain occurrence and their number. Bromodomain-containing proteins in Arabidopsis differ strikingly from animal bromodomain proteins with respect to the numbers of bromodomains and the other types of domains that are present. The substantial diversification of HATs and HDACs that has occurred since the divergence of plants, animals and fungi suggests a surprising degree of evolutionary plasticity and functional diversification in these core chromatin components.     

A conserved motif common to the histone acetyltransferase Esa1 and the histone deacetylase Rpd3

Post-translational modification of histones enables dynamic regulation of chromatin structure in eukaryotes. Histone acetyltransferase (HAT) and histone deacetylase (HDAC) modify the N-terminal tails of histones by adding or removing acetyl groups to specific lysine residues. A particular pair of HAT (Esa1) and HDAC (Rpd3) is proposed to modify the same lysine residue in vitro and in vivo. Thus, HAT and HDAC might have similar structural and functional motifs. Here we show that HAT (Esa1 family) and HDAC (Rpd3 family) have similar amino acid stretches in the primary structures through evolution. We refer to this region as the "ER (Esa1-Rpd3) motif." In the tertiary structure of Esa1, the ER motif is located near the active center. In Rpd3, for which the tertiary structure remains unclear, we demonstrate that the ER motif contains the same secondary structure as found in Esa1 by circular dichroism analysis. We did alanine-scanning mutagenesis and found that the ER motif regions of Esa1 or Rpd3 are required for HAT activity of Esa1 or HDAC activity of Rpd3, respectively. Our discovery of the ER motif present in the pair of enzymes (HAT and HDAC) indicates that HAT and HDAC have common structural bases, although they catalyze the reaction with opposite functions.     

葡萄COR27基因的克隆与抗寒功能研究

冬季低温是制约我国葡萄和葡萄酒产业发展的主要因素之一,揭示葡萄在冷胁迫下的信号转导通路、挖掘抗寒相关基因并解析其功能,对高耐寒品种的培育具有重要的理论和应用价值。本研究在欧亚种‘玫瑰香’葡萄(Vitis vinifera L.‘Muscat Hamburg’)冷胁迫相关转录组分析的基础上,鉴定了一个抗寒候选基因,通过同源性分析将其命名为VvCOR27。VvCOR27基因的cDNA序列(1082 bp)中,其开放阅读框(ORF)为909 bp,编码302个氨基酸。同源性分析显示,13个物种的COR27蛋白均具有3个特有的保守结构域。定量RT-PCR分析表明,VvCOR27在4℃低温处理24 h后大量表达。基于基因组序列的启动子基序分析表明,VvCOR27启动子区均只含有1个EE、EEL、G-box、ABREL元件,其数量少于AtCOR27,这可能是VvCOR27响应冷胁迫较AtCOR27滞后的原因。对3个超表达VvCOR27转基因拟南芥株系的抗寒性鉴定表明,VvCOR27参与了植株对冷胁迫的应答并作为正调控因子增强了植株对冷胁迫的耐受能力。     

葡萄白藜芦醇合酶基因的克隆及序列分析

目的:从葡萄中克隆白藜芦醇合酶基因vrs1并对其序列进行生物信息学分析.方法:利用葡萄总RNA为模板,采用RT - PCR技术克隆白藜芦醇合酶基因vrs1并亚克隆进T- Vector.利用生物信息学工具对其核酸和蛋白序列进行分析.结果:测序结果显示其cDNA序列全长为1 257bp,含有一个1 179bp的开放阅读框.生物信息学分析表明葡萄白藜芦醇合酶基因编码392个氨基酸,分子量为42.9kDa,理论等电点为5.97,具有芪合酶家族固有的氨基酸保守结构域,二级结构主要由α-螺旋、无规则卷曲、延伸链和β-转角组成.结论:该基因的克隆、生物信息学分析为进一步研究其功能奠定了基础.     

Sugars and Organic Acids of Vitis vinifera

Glucose, fructose, galactose, sucrose, maltose, melibiose, raffinose, and stachyose were identified in the leaves, bark, roots, and berries of Vitis vinifera L. var. Thompson Seedless. In addition to these sugars, verbascose and manninotriose were found in the leaves and bark.

Malic, tartaric, citric, isocitric, ascorbic, cis-aconitic, oxalic, glycolic, glyoxylic, succinic, lactic, glutaric, fumaric, pyrrolidone carboxylic, α-ketoglutaric, pyruvic, oxaloacetic, galacturonic, glucuronic, shikimic, quinic, chlorogenic, and caffeic acids were identified in the leaves, bark, roots, and berries.

Glucose, fructose, sucrose, malate, tartrate, and citrate were determined quantitatively in the leaf, petiole, xylem, bark, tendril, bud, puduncle pedicel, berry, lateral roots, and main roots at 4 separate physiological stages of growth. In addition, changes in the concentrations of fructose, glucose, malate, and tartrate in leaves were measured during a 36-day period starting from budburst.

     

葡萄VvBAP1基因的克隆及表达特性分析

以抗性葡萄品种‘F-242’组培苗为材料, 利用同源克隆法克隆了葡萄VvBAP1基因。测序结果显示, VvBAP1扩增片段大小为531 bp, 可编码176个氨基酸序列。利用生物信息学分析VvBAP1基因编码的蛋白序列显示, 该蛋白分子量为19.43 kDa, 含有保守的钙离子依赖性的C2结构域; 等电点pI为9.42; 不稳定系数为37.09, 推测为稳定的亲水性蛋白; 含有多个丝氨酸/苏氨酸磷酸化位点。实时荧光定量PCR表明, 该基因在根茎叶中均有表达, 其中在叶片中表达量较高; 盐胁迫、低温等逆境因子及逆境相关的信号物质, 如水杨酸和一氧化氮均可诱导VvBAP1的表达, 其中低温对其表达量影响更为显著, 推测该基因参与了葡萄抵御逆境胁迫的过程, 尤其是与低温相关的过程。     

Molecular linkage maps of Vitis vinifera L. and Vitis riparia Mchx

Two linkage maps for grape (Vitis spp.) have been developed based on 81 F(1) plants derived from an interspecific cross between the wine cultivar Moscato bianco (Vitis vinifera L.) and a Vitis riparia Mchx. accession, a donor of pathogen resistance traits. The double pseudotest-cross mapping strategy was applied using three types of molecular markers. The efficiency of SSRs to anchor homologous linkage groups from different Vitis maps and the usefulness of AFLPs in saturating molecular linkage maps were evaluated. Moreover, the SSCP technique was developed based on sequence information in public databases concerning genes involved in flavonoid and stilbene biosynthesis. For the maternal genetic map a total of 338 markers were assembled in 20 linkage groups covering 1,639 cM, whereas 429 loci defined the 19 linkage groups of the paternal map which covers 1,518 cM. The identification of 14 linkage groups common to both maps was possible based on 21 SSR and 19 AFLP loci. The position of SSR loci in the maps presented here was consistent with other published mapping experiments in Vitis.     

Genetic transformation of Vitis vinifera via organogenesis

Background  

Efficient transformation and regeneration methods are a priority for successful application of genetic engineering to vegetative propagated plants such as grape. The current methods for the production of transgenic grape plants are based on Agrobacterium-mediated transformation followed by regeneration from embryogenic callus. However, grape embryogenic calli are laborious to establish and the phenotype of the regenerated plants can be altered.     

Physiological Change and Transcriptome Analysis of Chinese Wild Vitis amurensis and Vitis vinifera in Response to Cold Stress

Plant Molecular Biology Reporter - The Chinese wild Vitis amurensis Rupr. is a crucial resource for cold-resistant germplasm, but the molecular mechanism of cold resistance in V. amurensis has not...     

Phases of Berry Growth in Vitis vinifera

The course of berry growth in Vitis vinifera has been interpreteddifferently by various authors. Divisions into two, three orfour phases have been postulated, though, in the latter cases,without any objective criteria for their delimitation. To clarifythis point, investigations were carried out with the cultivarsBacchus and Madeleine. Fresh and dry wt curves showed a double sigmoid course and threetransition points could be clearly defined. The central transitionpoint, occurring around 42 d after anthesis, may be definedas the change-over from the first to the second growth phase.Both the course of the fresh weight curve when plotted logarithmicallyand the relative growth rates argue against there being a phaseof slow growth at the beginning of the first growth phase. Indeed,the relative increase in fresh weight is maximal at the beginningof the first growth phase. The delimitation of a separate phase of little or no growthin the region of the transition from the first to the secondgrowth phase is not supported. The definitions of such phaseboundaries is arbitrary. The smaller the number of seeds perberry, the earlier is the first growth phase ended and the secondgrowth phase, including veraison, begun. During the first growth phase there is high cell division activity.The average area of an epidermal cell reached its minimum at8–11 d after anthesis, with a simultaneous strong increasein cell number. The maximal number of epidermal cells was attainedtowards the end of the first growth phase. The growth of the embryo showed no relation to the double-sigmoidalgrowth of the pericarp. Final embryo size was reached at 70–75d after anthesis. Seed d. wt, on the other hand, showed a biphasicincrease. The results presented here support the division of berry growthof V. vinifera into just two phases. Vitis vinifera L., grape vine, berry growth, growth phases     

Der Mitosezyklus der Zygotenkerne von Vitis vinifera

Bei Vitis vinifera cv. Weißer Burgunder und cv. Gewürztraminer wurde in zwei Jahren der Ablauf des Mitosezyklus der Zygoten untersucht. Anhand der Kernvolumina konnte festgestellt werden, daß die Befruchtung innerhalb von 24 Stunden nach dem Öffnen der Blüten (Bestäubung) stattfindet. Die G₁-Phase dauerte bis zum achten Tag nach dem Aufblühen. Die S-Phase wurde in vier Tagen und die G₂-Phase in sechs Tagen durchlaufen. Die Mitose, einschließlich des Zerstäubungsstadiums, dauerte drei Tage. Der Mitosezyklus der Zygotenkerne von Vitis vinifera benötigte also 20 Tage. Gegen Ende dieser Zeit wurde das Endosperm zellulär und konnte die Ernährung des sich entwickelnden Embryos übernehmen.     

Characterization of potential ABA receptors in Vitis vinifera

Molecular control mechanisms for abiotic stress tolerance are based on the activation and regulation of specific stress-related genes. The phytohormone abscisic acid (ABA) is a key endogenous messenger in a plant’s response to such stresses. A novel ABA binding mechanism which plays a key role in plant cell signaling cascades has recently been uncovered. In the absence of ABA, a type 2C protein phosphatase (PP2C) interacts and inhibits the kinase SnRK2. Binding of ABA to the PYR/PYLs receptors enables interaction between the ABA receptor and the PP2C protein, and abrogates the SnRK2 inactivation. The active SnRK2 is then free to activate the ABA-responsive element Binding Factors which target ABA-dependent gene expression. We used the grape as a model to study the ABA perception mechanism in fruit trees. The grape ABA signaling cascade consists of at least seven ABA receptors and six PP2Cs. We used a yeast two-hybrid system to examine physical interaction in vitro between the grape ABA receptors and their interacting partners, and found that twenty-two receptor-PP2C interactions can occur. Moreover, quantifying these affinities by the use of the LacZ reporter enables us to show that VvPP2C4 and VvPP2C9 are the major binding partners of the ABA receptor. We also tested in vivo the root and leaf gene expression of the various ABA receptors and PP2Cs in the presence of exogenic ABA and under different abiotic stresses such as high salt concentration, cold and drought, and found that many of these genes are regulated by such abiotic environmental factors. Our results indicate organ specificity in the ABA receptor genes and stress specificity in the VvPP2Cs. We suggest that VvPP2C4 is the major PP2C involved in ABA perception in leaves and roots, and VvRCAR6 and VvRCAR5 respectively, are the major receptors involved in ABA perception in these organs. Identification, characterization and manipulation of the central players in the ABA signaling cascades in fruit trees is likely to prove essential for improving their performance in the future.     

Antioxidant and Antiproliferative Activities of Twenty-Four Vitis vinifera Grapes

Grapes are rich in phytochemicals with many proven health benefits. Phenolic profiles, antioxidant and antiproliferative activities of twenty-four selected Vitis vinifera grape cultivars were investigated in this study. Large ranges of variation were found in these cultivars for the contents of total phenolics (95.3 to 686.5 mg/100 g) and flavonoids (94.7 to 1055 mg/100 g) and antioxidant activities (oxygen radical absorbance capacity 378.7 to 3386.0 mg of Trolox equivalents/100 g and peroxylradical scavenging capacity14.2 to 557 mg of vitamin C equivalents/100 g), cellular antioxidant activities (3.9 to 139.9 µmol of quercetin equivalents/100 g without PBS wash and 1.4 to 95.8 µmol of quercetin equivalents /100 g with PBS wash) and antiproliferative activities (25 to 82% at the concentrations of 100 mg/mL extracts).The total antioxidant activities were significantly correlated with the total phenolics and flavonoids. However, no significant correlations were found between antiproliferative activities and total phenolics or total flavonoids content. Wine grapes and color grapes showed much higher levels of phytochemicals and antioxidant activities than table grapes and green/yellow grapes. Several germplasm accessions with much high contents of phenolics and flavonoids, and total antioxidant activity were identified. These germplasm can be valuable sources of genes for breeding grape cultivars with better nutritional qualities of wine and table grapes in the future.     

Gibberellin-like substances in root exudate of Vitis vinifera

Summary The levels of gibberellin (GA)-like activity in the root exudate of two seedless varieties of Vitis vinifera were examined by the barley endosperm assay, and compared with levels determined for other parts of the plant. That activity was due to GA-like substances was confirmed with dwarf-5 corn.When acidic, ethyl acetate soluble GA-like substances from sap and leaf extracts were chromatogrammed on thin layers of silica gel in chloroform/ethyl acetate/formic acid (50:50:1), activity moved to the same Rf as GA₃ and GA₁ (Rf 0.05–0.25). However, substances inhibitory to the barley endosperm assay were detected in both sap and leaf extracts. In the above solvent system the inhibitor(s) co-chromatogrammed with a GA₁/GA₇ mixture, and with abscisin II. The GA-like activity co-chromatogrammed with GA₃ on paper developed in isopropanol/ammonia/water (10:1:1).Calculations on the rate of gibberellin movement from the roots seemed to be compatible with levels of activity in the leaves, although these levels could also be a reflection of the general gibberellin level in the plant.The relevance of the findings is discussed.     

Immunocharacterization of NADH-Glutamate Dehydrogenase from Vitis vinifera L

Rabbit antiserum was raised against NADH-glutamate dehydrogenase (GDH) isoenzyme 1, purified from leaves of Vitis vinifera L. cv Soultanina and its specificity was tested. This antiserum was used for immunocharacterization of the GDH from leaf, shoot, and root tissues. The antiserum recognized the seven isoenzymes of NADH-GDH and precipitated all the enzyme activity from the three tissues tested. Western blot following SDS-PAGE revealed the same protein band for the three tissues, with a molecular mass of 42.5 kilodaltons corresponding to NADH-GDH subunit. Results, based on the immunological studies, revealed that NADH-GDH from leaf, shoot, and root tissues are closely related proteins. Furthermore, addition of ammonium ions to the culture medium of in vitro grown explants resulted in a significant increase in NADH-GDH activity in root, shoot, and leaf tissues.