Prediction and analysis of protein palmitoylation sites.

Palmitoylation is a universal and important lipid modification, involving a series of basic cellular processes, such as membrane trafficking, protein stability and protein aggregation. With the avalanche of new protein sequences generated in the post genomic era, it is highly desirable to develop computational methods for rapidly and effectively identifying the potential palmitoylation sites of uncharacterized proteins so as to timely provide useful information for revealing the mechanism of protein palmitoylation. By using the Incremental Feature Selection approach based on amino acid factors, conservation, disorder feature, and specific features of palmitoylation site, a new predictor named IFS-Palm was developed in this regard. The overall success rate thus achieved by jackknife test on a newly constructed benchmark dataset was 90.65%. It was shown via an in-depth analysis that palmitoylation was intimately correlated with the feature of the upstream residue directly adjacent to cysteine site as well as the conservation of amino acid cysteine. Meanwhile, the protein disorder region might also play an import role in the post-translational modification. These findings may provide useful insights for revealing the mechanisms of palmitoylation.

Comparison of phenolic acids and flavan-3-ols during wine fermentation of grapes with different harvest times.

To explore the effects of harvest time on phenolic compounds during wine fermentation, grape berries (Vitis vinifera L. cv. Vidal) were harvested at 17.5, 22.8 and 37.2 masculine Brix and were used to make dry wine, semi-sweet wine and icewine with low alcohol levels, respectively. Phenolic acids and flavan-3-ols were assayed during the fermentation of wines by means of reverse phase-high performance liquid chromatography (RP-HPLC). The results showed that concentrations of most of the phenolic acids and flavan-3-ol in musts increased with harvest time delay and higher total levels of these species were detected in all wines, compared with those measured before fermentation (the total phenolic acid content in wines was 1.5-2.0 fold that of in musts). Except for p-coumaric acid and (-)-epicatechin, other phenolic acids and flavan-3-ols had similar variation patterns (wave-like rise) during fermentation in dry wine and semi-sweet wine. However, some detected compounds, including gentisic acid, p-hydroxybenzoic acid, caffeic acid, p-coumaric acid and sinapic acid showed obviously different trends from the other two wines in the icewine making process. It is thus suggested that the harvest time has a decisive effect on phenols in final wines and influences the evolution of phenolic acids and flavan-3-ols during wine fermentation.

Involvement of phospholipase D in the low temperature acclimation-induced thermotolerance in grape berry.

Both phospholipase D (PLD, EC 3.1.4.4) and salicylic acid (SA) play important roles in response to external stimulation and activating defense system in plants. However, roles of the two signals in plants during the development of thermotolerance induced by low temperature acclimation remain unclear. In the experiment presented in the paper, grape berries (Vitis vinifera L. cv. Chardonnay) were pretreated at 8 degrees C for 3h and then transferred to 45 degrees C for heat stress. Compared with the control without low temperature pretreatment, membrane permeability and malondialdehyde (MDA) contents were reduced and the expression of HSP73 increased in the low temperature-pretreated berries under heat stress. During low temperature acclimation, PLD, SA and HSP73 could be activated. Meanwhile, the expression of HSP73 and the accumulation of free SA induced by low temperature can be inhibited by PLD activity inhibitor. All these results suggest that the activation of PLD is an early response to low temperature, and it is involved in the accumulation of free SA and the development of thermotolerance induced by low temperature acclimation.

Prokaryotic expression, polyclonal antibody preparation of the stilbene synthase gene from grape berry and its different expression in fruit development and under heat acclimation.

Stilbene synthase (STS, EC 2.3.1.95) leads to the production of resveratrol compounds, which are major components of the phytoalexin response against fungal pathogens of the plant and are highly bioactive substances of pharmaceutical interest. STS expression and regulation are important. Temperature is one of the main external factors affecting phytoalexin accumulation in plant tissues, the effect of temperature on resveratrol synthesis and stilbene synthase expression in grape berries has not been reported before. Here we cloned the full-length sts cDNA with 1179bp from grape berry via PCR, and then introduced into an expressed plasmid pET-30a(+) vector at the EcoRI and XhoI restriction sites. With the isopropyl-beta-d-thiogalactoside (IPTG) induced, the pET-sts was highly expressed in Escherichia coli BL21 (DE3) pLysS cells. A fusion protein with the His-Tag was purified by Ni-NTA His.Bind Resin and then used as the antigen to immunize a New Zealand rabbit. Furthermore, the antiserum was precipitated by 50% saturated ammonium sulfate and DEAE-Sephadex A-50 chromatography to obtain the immunoglobulin G (IgG) fraction. These results provide a substantial basis for the further studies of the STS in grape berry as well as in other species of plants. The sts expression in fruit development and in response to heat acclimation was then assayed. The results indicated STS was regulated in fruits depending on the developmental stage and significantly accumulation of STS mRNA and synthesis of new STS protein during the early of heat acclimation, this work offers an important basis for further investigating the mechanism of post-harvest fruit adaptation to environmental stresses.

Cloning of phospholipase D from grape berry and its expression under heat acclimation.

To investigate whether phospholipase D (PLD, EC 3.1.4.4) plays a role in adaptive response of post-harvest fruit to environment, a PLD gene was firstly cloned from grape berry (Vitis Vinifera L. cv. Chardonnay) using RT-PCR and 3'- and 5'-RACE. The deduced amino acid sequence (809 residues) showed 84.7% identity with that of PLD from Ricinus communis. The secondary structures of this protein showed the characteristic C2 domain and two active sites of a phospholipid-metabolizing enzyme. The PLD activity and its expression in response to heat acclimation were then assayed. The results indicated PLD was significantly activated at enzyme activity, as well as accumulation of PLD mRNA and synthesis of new PLD protein during the early of heat acclimation, primary suggesting that the grape berry PLD may be involved in the heat response in post-harvest grape berry. This work offers an important basis for further investigating the mechanism of post-harvest fruit adaptation to environmental stresses.

Expression of the chalcone synthase gene from grape and preparation of an anti-CHS antibody.

Flavonoids are closely related to a plant's antioxidative ability. Because chalcone synthase (CHS) is the first enzyme to act as part of the flavonoid biosynthesis pathway, its expression and regulation are important. Here we present the expression of a full-length chs cDNA with 1225bp from grape seedlings as well as the preparation of an antibody against the expressed protein. A full-length chs cDNA was introduced into an expressed plasmid pET-30a(+) vector at the EcoRI and SalI restriction sites. pET-chs was found to be highly expressed in Escherichia coli BL21(DE3) pLysS cells with isopropyl-beta-d-thiogalactoside (IPTG) induction. A fusion protein with the His.tag label was purified by Ni-NTA His. Bind Resin and then used as the antigen to immunize a New Zealand rabbit. The resulting antiserum was then further precipitated by 50% saturated ammonium sulfate and DEAE-Sepharose FF column chromatography to obtain the immunoglobulin G (IgG) fraction. The resulting antibody was found capable of immuno-recognizing the CHS of the crude protein extracts from different grape tissues with a molecular mass of 43kDa.

Contributions of PIP(2)-specific-phospholipase C and free salicylic acid to heat acclimation-induced thermotolerance in pea leaves.

The relationship between the accumulation in endogenous free salicylic acid (SA) induced by heat acclimation (37 degrees C) and the activity of PIP(2)-phospholipase C (PIP(2)-PLC; EC 3.1.4.3) in the plasma membrane fraction was investigated in pea (Pisum sativum L.) leaves. We focused our attention on the hypothesis that positive SA signals induced by heat acclimation may be relayed by PIP(2)-PLC. Heat acclimation induced an abrupt elevation of free SA preceding the activation of PLC toward PIP(2). Immunoblotting indicated a molecular mass with 66.5kDa PLC plays key role in the development of thermotolerance in pea leaves. In addition, some characterizations of PLC toward PIP(2) isolated from pea leaves with two-phase purification containing calcium concentration, pH and a protein concentration were also studied. Neomycin sulfate, a well-known PIP(2)-PLC inhibitor, was employed to access the involvement of PIP(2)-PLC in the acquisition of heat acclimation induced-thermotolerance. We were able to identify a PIP(2)-PLC, which was similar to a conventional PIP(2)-PLC in higher plants, from pea leaves suggesting that PIP(2)-PLC was involved in the signal pathway that leads to the acquisition of heat acclimation induced-thermotolerance. On the basis of these results, we conclude that the involvement of free SA may function as the upstream event in the stimulation of PIP(2)-PLC in response to heat acclimation treatment.

Changes and subcellular localizations of the enzymes involved in phenylpropanoid metabolism during grape berry development.

The phenylpropanoid pathway yields a variety of phenolics that are closely associated with fruit qualities in addition to structural and defense-related functions. However, very little has been reported concerning its metabolism in fruit. This experiment was designed to assess changes of eleven phenolic acids in grape berry (Vitis vinifera L. cv. Cabernet Sauvignon) and explore both the activities and amounts of three key enzymes--phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H) and 4-coumarate:coenzyme A ligase (4CL)--catalyzing the biosynthesis of these compounds during berry development. Finally, the subcellular localizations of the enzymes within berry tissues were also investigated using immuno-gold electron microscopic technique. The results indicated that the contents of gallic, protocatechuic, gentisic and caffeic acid all changed drastically during berry development, while other compounds containing p-hydroxybenzoic, vanillic, syringic, chlorogenic, p-coumaric, ferulic and sinapic acid varied only slightly. Activities of PAL, C4H and 4CL showed similar pattern changes with two accumulated peaks throughout berry development. In addition, their activities all showed a highly positive correlation with the total contents of phenolic acids, whereas the immunoblotting analysis showed that changes in enzyme activities were independent of the enzyme amounts. Results from the subcellular-localization study revealed that PAL was mainly present in the cell walls, secondarily thickened walls, and the parenchyma cells of the berry mesocarp cells, C4H was found primarily in the chloroplast (plastid) and nucleus and 4CL predominantly in the secondarily thickened walls and the parenchyma cells of mesocarp vascular tissue.