A quantitative portrait of three xylanase inhibiting protein families in different wheat cultivars using 2D-DIGE and multivariate statistical tools

Comprehensive genome-wide analysis of wheat xylanase inhibitor protein (XIP) genes: unveiling their role in Fusarium head blight resistance and plant immune mechanisms

In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.

Investigating phenotypic relationships in persimmon accessions through integrated proteomic and metabolomic analysis of corresponding fruits

Together with phenological and genomic approaches, gel-based and label-free proteomic as well metabolomic procedures were separately applied to plants to highlight differences between ecotypes, to estimate genetic variability within/between organism populations, or to characterize specific mutants/genetically modified lines at metabolic level. To investigate the possible use of tandem mass tag (TMT)-based quantitative proteomics in the above-mentioned contexts and based on the absence of combined proteo-metabolomic studies on Diospyros kaki cultivars, we here applied integrated proteomic and metabolomic approaches to fruits from Italian persimmon ecotypes with the aim to characterize plant phenotypic diversity at molecular level. We identified 2255 proteins in fruits, assigning 102 differentially represented components between cultivars, including some related to pomological, nutritional and allergenic characteristics. Thirty-three polyphenols were also identified and quantified, which belong to hydroxybenzoic acid, flavanol, hydroxycinnamic acid, flavonol, flavanone and dihydrochalcone sub-classes. Heat-map representation of quantitative proteomic and metabolomic results highlighted compound representation differences in various accessions, whose elaboration through Euclidean distance functions and other linkage methods defined dendrograms establishing phenotypic relationships between cultivars. Principal component analysis of proteomic and metabolomic data provided clear information on phenotypic differences/similarities between persimmon accessions. Coherent cultivar association results were observed between proteomic and metabolomic data, emphasizing the utility of integrating combined omic approaches to identify and validate phenotypic relationships between ecotypes, and to estimate corresponding variability and distance. Accordingly, this study describes an original, combined approach to outline phenotypic signatures in persimmon cultivars, which may be used for a further characterization of other ecotypes of the same species and an improved description of nutritional characteristics of corresponding fruits.

Friend or Foe? Impacts of Dietary Xylans, Xylooligosaccharides, and Xylanases on Intestinal Health and Growth Performance of Monogastric Animals

This paper discusses the structural difference and role of xylan, procedures involved in the production of xylooligosaccharides (XOS), and their implementation into animal feeds. Xylan is non-starch polysaccharides that share a β-(1-4)-linked xylopyranose backbone as a common feature. Due to the myriad of residues that can be substituted on the polymers within the xylan family, more anti-nutritional factors are associated with certain types of xylan than others. XOS are sugar oligomers extracted from xylan-containing lignocellulosic materials, such as crop residues, wood, and herbaceous biomass, that possess prebiotic effects. XOS can also be produced in the intestine of monogastric animals to some extent when exogenous enzymes, such as xylanase, are added to the feed. Xylanase supplementation is a common practice within both swine and poultry production to reduce intestinal viscosity and improve digestive utilization of nutrients. The efficacy of xylanase supplementation varies widely due a number of factors, one of which being the presence of xylanase inhibitors present in common feedstuffs. The use of prebiotics in animal feeding is gaining popularity as producers look to accelerate growth rate, enhance intestinal health, and improve other production parameters in an attempt to provide a safe and sustainable food product. Available research on the impact of xylan, XOS, as well as xylanase on the growth and health of swine and poultry, is also summarized. The response to xylanase supplementation in swine and poultry feeds is highly variable and whether the benefits are a result of nutrient release from NSP, reduction in digesta viscosity, production of short chain xylooligosaccharides or a combination of these is still in question. XOS supplementation seems to benefit both swine and poultry at various stages of production, as well as varying levels of XOS purity and degree of polymerization; however, further research is needed to elucidate the ideal dosage, purity, and degree of polymerization needed to confer benefits on intestinal health and performance in each respective species.

Superior Growth Rates in Broilers Fed Wheat with Low In Vitro Feed-Xylanase Inhibition

Grain-batch variation in xylanase-inhibitor levels may account for variations in the efficacy of feed xylanase supplementation. This would make inhibition an important quality parameter in the routine analysis of feedstuffs. Two analytical procedures for testing feedstuffs against specific xylanases were researched: the high-throughput viscosity-pressure assay (ViPr) and the extraction-free remazol-brilliant-blue-beechwood-xylan (RBBX) assay. Thirty-two wheat cultivars were analyzed for inhibition of a commercial xylanase, Ronozyme WX. Four cultivars were selected for a feeding experiment in which the growth of 1440 broilers from ages 7-33 days was monitored. The treatments resulted up to 7 % difference (day 14) in broiler weight . The cultivar choice had an effect throughout the experiment ( p < 0.05). The performance ranking of the treatments corresponded better to xylanase inhibition than to crude-protein content or nonstarch-polysaccharide content. Wheat-grain xylanase-inhibitor content is therefore a highly relevant quality parameter when broiler diets are supplemented with feed xylanase.

Comparative proteomic analysis of Dan'er malts produced from distinct malting processes by two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE)

The malting process is the controlled germination, followed by drying, of the barley grain. For brewing beer, the malting process is modified according to the features of the barley variety being malted. In China, there are two schedules routinely used for malting the widely grown Dan'er cultivar, processes I and II. The quality of malt produced with process II is considered to be superior to that from process I for Dan'er by maltsters and brewers. In the present study, comparative proteomic analysis was performed between Dan'er malts produced by malting processes I and II. The data showed that enzymes and proteins responsible for cell wall polysaccharide degradation and starch and protein hydrolysis were more abundant in malt produced by process II, leading to improved quality, especially for the commercially important filterability, saccharification time, and diastatic power (DP) quality traits. In addition, to verify the proteomic results, the activities of several key enzymes (α-amylase, β-amylase, and limit dextrinase) were compared between the two malts. This enabled the influence of malting process on malt quality to be determined and suggested malting process schedule changes to optimize the malting process for the Dan'er cultivar, especially for improving filterability, which is often deemed as suboptimal by maltsters and brewers.

Proteomic analysis of differences in barley (Hordeum vulgare) malts with distinct filterability by DIGE

Filterability is an essential quality parameter of barley malt and significantly impacts productive efficiency and quality of beer. In the study, differences of metabolic capability, rather than of initial contents of macromolecules in barleys, were found to be the main reason for malt filterability gap between the widely used cultivars Dan'er and Metcalfe in China. Comparative proteomics based on fluorescent difference gel electrophoresis (DIGE) was employed to quantitatively analyze proteins of four commercial malts belonging to the two cultivars, and 51 cultivar-differential spots were identified to 40 metabolic proteins by MALDI-TOF/TOF mass spectrometry, mainly including hydrolases and pathogen-related proteins. According to their function analysis and abundance comparison between cultivars, filterability-beneficial and -adverse proteins were putatively proposed. Two most remarkable differential proteins, β-amylase and serpin Z7, were further investigated to verify their effects on Dan'er malt filterability. These results provide biological markers for barley breeders and maltsters to improve malt filterability.

BIOLOGICAL SIGNIFICANCE

To the best of our knowledge, this is the first report of comprehensive investigation of metabolic proteins related to wort filterability of barley malts, and sheds light on clues for filterability improvement. Visible differences in the expression level of metabolic proteins between Dan'er and Metcalfe malts using 2D-DIGE signify a valuable tool for cultivar comparison, illustration of key proteins responsible for filterability and even other qualities of barley malts. And with these explorations on biomarkers of malt filterability and other aspects, there will be higher efficiency and quality of beer brewing, less application of exogenous hydrolases and more expending market for Chinese malting barleys. This article is part of a Special Issue entitled: Translational Plant Proteomics.

From protein catalogues towards targeted proteomics approaches in cereal grains

Due to their importance for human nutrition, the protein content of cereal grains has been a subject of intense study for over a century and cereal grains were not surprisingly one of the earliest subjects for 2D-gel-based proteome analysis. Over the last two decades, countless cereal grain proteomes, mostly derived using 2D-gel based technologies, have been described and hundreds of proteins identified. However, very little is still known about post-translational modifications, subcellular proteomes, and protein-protein interactions in cereal grains. Development of techniques for improved extraction, separation and identification of proteins and peptides is facilitating functional proteomics and analysis of sub-proteomes from small amounts of starting material, such as seed tissues. The combination of proteomics with structural and functional analysis is increasingly applied to target subsets of proteins. These "next-generation" proteomics studies will vastly increase our depth of knowledge about the processes controlling cereal grain development, nutritional and processing characteristics.

2-D DIGE reveals changes in wheat xylanase inhibitor protein families due to Fusarium graminearum DeltaTri5 infection and grain development

Wheat contains three different classes of proteinaceous xylanase inhibitors (XIs), i.e. Triticum aestivum xylanase inhibitors (TAXIs) xylanase-inhibiting proteins (XIPs), and thaumatin-like xylanase inhibitors (TLXIs) which are believed to act as a defensive barrier against phytopathogenic attack. In the absence of relevant data in wheat kernels, we here examined the response of the different members of the XI protein population to infection with a DeltaTri5 mutant of Fusarium graminearum, the wild type of which is one of the most important wheat ear pathogens, in early developing wheat grain. Wheat ears were inoculated at anthesis, analyzed using 2-D DIGE and multivariate analysis at 5, 15, and 25 days post anthesis (DPA), and compared with control samples. Distinct abundance patterns could be distinguished for different XI forms in response to infection with F. graminearum DeltaTri5. Some (iso)forms were up-regulated, whereas others were down-regulated. This pathogen-specific regulation of proteins was mostly visible at five DPA and levelled off in the samples situated further from the inoculation point. Furthermore, it was shown that most identified TAXI- and XIP-type XI (iso)forms significantly increased in abundance from the milky (15 DPA) to the soft dough stages (25 DPA) on a per kernel basis, although the extent of increase differed greatly. Non-glycosylated XIP forms increased more strongly than their glycosylated counterparts.