Steven C. Van Sluyter

Less label, more free: Approaches in label-free quantitative mass spectrometry

In this review we examine techniques, software, and statistical analyses used in label‐free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label‐free quantitation. Limitations of label‐free approaches are considered, label‐free approaches are compared with labelling techniques, and forward‐looking applications for label‐free quantitative data are presented. We conclude that label‐free quantitative proteomics is a reliable, versatile, and cost‐effective alternative to labelled quantitation.

Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit

BackgroundCabernet Sauvignon grapevines were exposed to a progressive, increasing water defict over 16 days. Shoot elongation and photosynthesis were measured for physiological responses to water deficit. The effect of water deficit over time on the abundance of individual proteins in growing shoot tips (including four immature leaves) was analyzed using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS).ResultsWater deficit progressively decreased shoot elongation, stomatal conductance and photosynthesis after Day 4; 2277 proteins were identified by shotgun proteomics with an average CV of 9% for the protein abundance of all proteins. There were 472 out of 942 (50%) proteins found in all samples that were significantly affected by water deficit. The 472 proteins were clustered into four groups: increased and decreased abundance of early- and late-responding protein profiles. Vines sensed the water deficit early, appearing to acclimate to stress, because the abundance of many proteins changed before decreases in shoot elongation, stomatal conductance and photosynthesis. Predominant functional categories of the early-responding proteins included photosynthesis, glycolysis, translation, antioxidant defense and growth-related categories (steroid metabolism and water transport), whereas additional proteins for late-responding proteins were largely involved with transport, photorespiration, antioxidants, amino acid and carbohydrate metabolism.ConclusionsProteomic responses to water deficit were dynamic with early, significant changes in abundance of proteins involved in translation, energy, antioxidant defense and steroid metabolism. The abundance of these proteins changed prior to any detectable decreases in shoot elongation, stomatal conductance or photosynthesis. Many of these early-responding proteins are known to be regulated by post-transcriptional modifications such as phosphorylation. The proteomics analysis indicates massive and substantial changes in plant metabolism that appear to funnel carbon and energy into antioxidant defenses in the very early stages of plant response to water deficit before any significant injury.

The Botrytis cinerea aspartic proteinase family.

The ascomycete plant pathogen Botrytis cinerea secretes aspartic proteinase (AP) activity. Functional analysis was carried out on five aspartic proteinase genes (Bcap1-5) reported previously. Single and double mutants lacking these five genes showed neither a reduced secreted proteolytic activity, nor a reduction in virulence and they showed no alteration in sensitivity to antifungal proteins purified from grape juice. Scrutiny of the B. cinerea genome revealed the presence of nine additional Bcap genes, denoted Bcap6-14. The product of the Bcap8 gene was found to constitute up to 23% of the total protein secreted by B. cinerea. Bcap8-deficient mutants secreted approximately 70% less AP activity but were just as virulent as the wild-type strain. Phylogenetic analysis showed that Bcap8 has orthologs in many basidiomycetes but only few ascomycetes including the biocontrol fungus Trichoderma harzanium. Potential functions of the 14 APs in B. cinerea are discussed based on their sequence characteristics, phylogeny and predicted localization.

Thermal Stability of Thaumatin-Like Protein, Chitinase, and Invertase Isolated from Sauvignon blanc and Semillon Juice and Their Role in Haze Formation in Wine

A thermal unfolding study of thaumatin-like protein, chitinase, and invertase isolated from Vitis vinifera Sauvignon blanc and Semillon juice was undertaken. Differential scanning calorimetry demonstrated that chitinase was a major player in heat-induced haze in unfined wines as it had a low melt temperature, and aggregation was observed. The kinetics of chitinase F1 (Sauvignon blanc) unfolding was studied using circular dichroism spectrometry. Chitinase unfolding conforms to Arrhenius behavior having an activation energy of 320 kJ/mol. This enabled a predictive model for protein stability to be generated, predicting a half-life of 9 years at 15 degrees C, 4.7 days at 30 degrees C, and 17 min at 45 degrees C. Circular dichroism studies indicate that chitinase unfolding follows three steps: an initial irreversible step from the native to an unfolded conformation, a reversible step between a collapsed and an unfolded non-native conformation, followed by irreversible aggregation associated with visible haze formation.

Roles of grape thaumatin-like protein and chitinase in white wine haze formation

Grape chitinase was found to be the primary cause of heat-induced haze formation in white wines. Chitinase was the dominant protein in a haze induced by treating Sauvignon blanc wine at 30 °C for 22 h. In artificial wines and real wines, chitinase concentration was directly correlated to the turbidity of heat-induced haze formation (50 °C for 3 h). Sulfate was confirmed to have a role in haze formation, likely by converting soluble aggregates into larger visible haze particles. Thaumatin-like protein was detected in the insoluble fraction by SDS-PAGE analysis but had no measurable impact on turbidity. Differential scanning calorimetry demonstrated that the complex mixture of molecules in wine plays a role in thermal instability of wine proteins and contributes additional complexity to the wine haze phenomenon.

Grape and Wine Proteins: Their Fractionation by Hydrophobic Interaction Chromatography and Identification by Chromatographic and Proteomic Analysis

A method to fractionate grape and wine proteins by hydrophobic interaction chromatography (HIC) was developed. This method allowed the isolation of a thaumatin-like protein in a single step with high yield and >90% purity and has potential to purify several other proteins. In addition, by separating HIC fractions by reverse phase HPLC and by collecting the obtained peaks, the grape juice proteins were further separated, by SDS-PAGE, into 24 bands. The bands were subjected to nanoLC-MS/MS analysis, and the results were matched against a database and characterized as various Vitis vinifera proteins. Moreover, either directly or by homology searching, identity or function was attributed to all of the gel bands identified, which mainly consisted of grape chitinases and thaumatin-like proteins but also included vacuolar invertase, PR-4 type proteins, and a lipid transfer protein from grapes.

Wine Protein Haze: Mechanisms of Formation and Advances in Prevention

Protein haze is an aesthetic problem in white wines that can be prevented by removing the grape proteins that have survived the winemaking process. The haze-forming proteins are grape pathogenesis-related proteins that are highly stable during winemaking, but some of them precipitate over time and with elevated temperatures. Protein removal is currently achieved by bentonite addition, an inefficient process that can lead to higher costs and quality losses in winemaking. The development of more efficient processes for protein removal and haze prevention requires understanding the mechanisms such as the main drivers of protein instability and the impacts of various wine matrix components on haze formation. This review covers recent developments in wine protein instability and removal and proposes a revised mechanism of protein haze formation.

Degradation of white wine haze proteins by Aspergillopepsin I and II during juice flash pasteurization

Bentonite is commonly used to remove grape proteins responsible for haze formation in white wines. Proteases potentially represent an alternative to bentonite, but so far none has shown satisfactory activity under winemaking conditions. A promising candidate is AGP, a mixture of Aspergillopepsins I and II.; a food grade, well characterized and inexpensive protease, active at wine pH and at high temperatures (60-80°C). AGP was added to two clarified grape juices with and without heat treatments (75°C, 1min) prior to fermentation. AGP showed some activity at fermentation temperatures (≈20% total protein reduction compared to control wine) and excellent activity when combined with juice heating (≈90% total protein reduction). The more heat stable grape proteins, i.e. those not contributing to wine hazing, were not affected by the treatments and therefore accounted for the remaining 10% of protein still in solution after the treatments. The main physicochemical parameters and sensorial characteristics of wines produced with AGP were not different from controls.

Roles of proteins, polysaccharides, and phenolics in haze formation in white wine via reconstitution experiments

Residual proteins in finished wines can aggregate to form haze. To obtain insights into the mechanism of protein haze formation, a reconstitution approach was used to study the heat-induced aggregation behavior of purified wine proteins. A chitinase, four thaumatin-like protein (TLP) isoforms, phenolics, and polysaccharides were isolated from a Chardonnay wine. The same wine was stripped of these compounds and used as a base to reconstitute each of the proteins alone or in combination with the isolated phenolics and/or polysaccharides. After a heating and cooling cycle (70 °C for 1 h and 25 °C for 15 h), the size and concentration of the aggregates formed were measured by scanning ion occlusion sensing (SIOS), a technique to detect and quantify nanoparticles. The chitinase was the protein most prone to aggregate and the one that formed the largest particles; phenolics and polysaccharides did not have a significant impact on its aggregation behavior. TLP isoforms varied in susceptibility to haze formation and in interactions with polysaccharides and phenolics. The work establishes SIOS as a useful method for studying wine haze.

Two-step purification of pathogenesis-related proteins from grape juice and crystallization of thaumatin-like proteins

Grape thaumatin-like (TL) proteins and chitinases play roles in plant-pathogen interactions and can cause protein haze in white wine unless removed prior to bottling. A two-step method is described that highly purified hundreds of milligrams of TL proteins and chitinases from two juices by strong cation exchange (SCX) and hydrophobic interaction chromatography (HIC). The method was fast and separated isoforms of TL proteins and chitinases from within the same juice, in most cases to >97% purity. The isolated proteins were identified by peptide nanoLC-MS/MS and crystallized using a high-throughput screening method. Crystals from three protein fractions produced high-resolution X-ray crystallography data.