Matrix-assisted laser desorption/ionization time-of-flight based wheat gliadin protein peaks are useful molecular markers for wheat genetic study

Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing

BACKGROUND

Wheat grain avenin-like proteins (ALPs) belong to a recently discovered class of wheat grain storage protein. ALPs in wheat grains not only have beneficial effects on dough quality but also display antifungal activities, which is a novel observation for wheat storage proteins. Previous studies have shown that ALPs are likely present in the albumin/globulin fractions of total protein extract from wheat flour. However, the accumulation characteristics of these ALPs in the mature wheat grain remains unknown.

RESULTS

In the present study, a total of 13 ALPs homologs were isolated and characterized in the albumin/globulin fractions of the wheat protein extract. A combination of multiple techniques including RP-HPLC, SDS-PAGE, MALDI-TOF and peptide sequencing were used for accurate separation and identification of individual ALP homolog. The C-terminal TaALP-by-4AL/7DS, TaALP-by-4AL/7AS/7DS, TaALP-bx/4AL/7AS/7DS, TaALP-ay-7DS, TaALP-ay-4AL, TaALP-ax-4AL, TaALP-ax-7AS, and TaALP-ax-7DS, were separated as individual protein bands from wheat flour for the first time. These unique ALPs peptides were mapped to the latest wheat genome assembly in the IWGSC database. The characteristic defence related proteins present in albumin and globulin fractions, such as protein disulfide-isomerase (PDI), grain softness protein (GSP), alpha-amylase inhibitors (AAIs) and endogenous alpha-amylase/subtilisin inhibitor were also found to co-segregate with these identified ALPs, avenin-3 and α-gliadins. The molecular weight range and the electrophoresis segregation properties of ALPs were characterised in comparison with the proteins containing the tryp_alpha_amyl domain (PF00234) and the gliadin domain (PF13016), which play a role in plant immunity and grain quality. We examined the phylogenetic relationships of the AAIs, GSP, avenin-3, α-gliadins and ALPs, based on the alignment of their functional domains. MALDI-TOF profiling indicated the occurrence of certain post-translations modifications (PTMs) in some ALP subunits.

CONCLUSIONS

We reported for the first time the complete profiling of ALPs present in the albumin/globulin fractions of wheat grain protein extracts. We concluded that majority of the ALPs homologs are expressed in wheat grains. We found clear evidence of PTMs in several ALPs peptides. The identification of both gliadin domain (PF13016) and Tryp_alpha_amyl domain (PF00234) in the mature forms of ALPs highlighted the multiple functional properties of ALPs in grain quality and disease resistance.

Two Novel Y-Type High Molecular Weight Glutenin Genes in Chinese Wheat Landraces of the Yangtze-River Region

High molecular weight glutenin subunits (HMW-GSs) are key determinants for the end-use quality of wheat. Chinese wheat landraces are an important resource for exploring novel HMW-GS genes to improve the wheat baking quality. Two novel Glu-1Dy HMW-GSs (designated as 1Dy12.6 and 1Dy12.7) were identified and cloned from two Chinese wheat landraces Huazhong830 and Luosimai. The 1Dy12.6 and 1Dy12.7 subunits were deposited as the NCBInr Acc. No KR262518, and KR262519, respectively. The full open reading frames (ORFs) of 1Dy12.6 and 1Dy12.7 were 2022 bp and 1977 bp, encoding for proteins of 673 and 658 amino acid residues, respectively. Each contains four typical primary regions of HMW-GSs (a signal peptide, N- and C-terminal regions, and a central repetitive region). Their deduced molecular masses (70,165 Da and 68,400 Da) were strikingly consistent with those identified by MALDI-TOF-MS (69,985Da and 68,407 Da). The 1Dy12.6 is the largest 1Dy glutenin subunits cloned in common wheat up to date, containing longer repetitive central domains than other 1Dy encoded proteins. In comparison with the most similar active 1Dy alleles previously reported, the newly discovered alleles contained a total of 20 SNPs and 3 indels. The secondary structure prediction indicated that 1Dy12.6 and 1Dy12.7 have similar proportion of α-helix, β-turn, and β-bend to those of 1Dy10 (X12929). The phylogenetic analysis illustrated that the x- and y-type subunits of glutenins were well separated, but both 1Dy12.6 and 1Dy12.7 were clustered with the other Glu-1Dy alleles. Our results revealed that the 1Dy12.6 and 1Dy12.7 subunit have potential to strengthen gluten polymer interactions, and are valuable genetic resources for wheat quality improvement.

Identification of chromosome regions controlling seed storage proteins of narrow-leafed lupin (Lupinus angustifolius)

Narrow-leafed lupin (Lupinus angustifolius L.) is a valuable legume crop for animal feed and human health food because of its high proteins content. However, the genetics of seed storage proteins is unclear, limiting further improvement of protein quantity and quality. In this study, matrix-assisted laser desorption/ionization time of flight mass spectrometry was used for the first time to analyze lupin seed storage proteins and the spectra generated was treated as markers to investigate the chromosome locations controlling seed storage proteins in the narrow-leafed lupin. In a recombinant inbred line population of 89 individuals, 48 polymorphic protein peaks were identified and seven of which were successfully mapped onto four existing linkage groups: two on NLL-04, three on NLL-05, one on NLL-07 and one on NLL-14, with LOD values ranging from 2.6 to 7.7 confirming a significant linkage. Most protein-based markers showed distorted segregation and were failed to be integrated into the reference map. Among them, 31 were grouped into six clusters and the other ten were totally unlinked. This study provides a significant clue to study the comparative genomics/proteomics among legumes as well as for protein marker-assisted breeding. The distribution pattern of genes controlling seed storage protein revealed in this study probably exists universally among legumes or even all plants and animals. Whether genes controlling seed storage protein share the same gene expression pattern controlling other enzymes and what is the mechanism behind it are the questions which remain to be answered in the future.

Differential recovery of lupin proteins from the gluten matrix in lupin-wheat bread as revealed by mass spectrometry and two-dimensional electrophoresis

Bread made from a mixture of wheat and lupin flour possesses a number of health benefits. The addition of lupin flour to wheat flour during breadmaking has major effects on bread properties. The present study investigated the lupin and wheat flour protein interactions during the breadmaking process including dough formation and baking by using proteomics research technologies including MS/MS to identify the proteins. Results revealed that qualitatively most proteins from both lupin and wheat flour remained unchanged after baking as per electrophoretic behavior, whereas some were incorporated into the bread gluten matrix and became unextractable. Most of the lupin α-conglutins could be readily extracted from the lupin-wheat bread even at low salt and nonreducing/nondenaturing extraction conditions. In contrast, most of the β-conglutins lost extractability, suggesting that they were trapped in the bread gluten matrix. The higher thermal stability of α-conglutins compared to β-conglutins is speculated to account for this difference.

Characterization and comparative analysis of wheat high molecular weight glutenin subunits by SDS-PAGE, RP-HPLC, HPCE, and MALDI-TOF-MS

High molecular weight glutenin subunits (HMW-GS) from 60 germplasms including 30 common wheat cultivars and 30 related species were separated and characterized by a suite of separation methods including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), reversed-phase high-performance liquid chromatography (RP-HPLC), high-performance capillary electrophoresis (HPCE), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Comparative analysis demonstrated that each methodology has its own advantages and disadvantages. The main drawback of SDS-PAGE was its overestimation of molecular mass and incorrect identification of HMW-GS due to its low resolution. However, it had the advantages of technical simplicity and low requirements of equipment; thus, it is suitable for large-scale and high-throughput HMW-GS screening for breeding programs, especially when the glutenin composition is clear in the breeding material. MALDI-TOF-MS clearly expressed many technical advantages among the four methods evaluated, including high throughput, high resolution, and accuracy; it was, however, associated with high equipment cost, thus preventing many breeding companies from accessing the technology. RP-HPLC and HPCE were found to be intermediate between SDS-PAGE and MALDI-TOF-MS. Both RP-HPLC and HPCE demonstrated higher resolution and reproducibility over SDS-PAGE but lower detection power than MALDI-TOF-MS. Results demonstrated that MALDI-TOF-MS is suitable for analyzing HMW-GS for routine breeding line screening and for identifying new genotypes.

Proteomic-based analytical approach for the characterization of glutenin subunits in durum wheat

One of the main objectives of wheat glutenin subunit (GS) analysis is the identification of protein components linked to wheat quality. The proteomic characterization of glutenin has to consider the relatively low levels of arginine and lysine residues and the close sequence similarity among the different groups of these subunits, which hinders or even prevents the identification of the GS. In this study, a proteomic approach has been applied to resolve the heterogeneity of wheat glutenin components. Proteins extracted from Triticum durum flour were first analyzed by two-dimensional gel electrophoresis, which greatly reduced glutenin complexity. The identity of each spot was confirmed by nano liquid chromatography tandem mass spectrometry analysis of tryptic peptides. In parallel, measurements of the high mass range by matrix-assisted laser desorption/ionization time-of-flight analysis allowed detection of the large tryptic peptides. Gathering all data from search engine interrogation, very high sequence coverage was obtained for high molecular weight GS, including Bx7 and By8, in agreement with the known genetic profile of durum wheat. In addition, a truncated form of By8, never detected before, was also found. Low molecular weight GS (LMW-GS) B-type was identified with reasonable sequence coverage, while a clear identification of LWM-GS C- and D-type was hindered by the incompleteness of the wheat DNA databases. This study represents the first comprehensive analysis of the glutenin proteome and provides a reliable method for classifying wheat varieties according to their glutenin profile.

Isolation of wheat–rye 1RS recombinants that break the linkage between the stem rust resistance gene SrR and secalin

Chromosome 1R of rye is a useful source of genes for disease resistance and enhanced agronomic performance in wheat. One of the most prevalent genes transferred to wheat from rye is the stem rust resistance gene Sr31. The recent emergence and spread of a stem rust pathotype virulent to this gene has refocused efforts to find and utilize alternative sources of resistance. There has been considerable effort to transfer a stem rust resistance gene, SrR, from Imperial rye, believed to be allelic to Sr31, into commercial wheat cultivars. However, the simultaneous transfer of genes at the Sec-1 locus encoding secalin seed storage proteins and their association with quality defects preclude the deployment of SrR in some commercial wheat breeding programs. Previous attempts to induce homoeologous recombination between wheat and rye chromosomes to break the linkage between SrR and Sec-1 whilst retaining the tightly linked major loci for wheat seed storage proteins, Gli-D1 and Glu-D3, and recover good dough quality characteristics, have been unsuccessful. We produced novel tertiary wheat–rye recombinant lines carrying different lengths of rye chromosome arm 1RS by inducing homoeologous recombination between the wheat 1D chromosome and a previously described secondary wheat–rye recombinant, DRA-1. Tertiary recombinant T6-1 (SrR+ Sec-1–) carries the target gene for stem rust resistance from rye and retains Gli-D1 but lacks the secalin locus. The tertiary recombinant T49-7 (SrR– Sec-1+) contains the secalin locus but lacks the stem rust resistance gene. T6-1 is expected to contribute to wheat breeding programs in Australia, whereas T49-7 provides opportunities to investigate whether the presence of secalins is responsible for the previously documented dough quality defects.

The influences of genotype, environment, and genotype×environment interaction on wheat quality

Knowledge of the relative contributions of genotype (G), environment (E), and genotype and environment interaction (G × E) effects on wheat (Triticum aestivum L.) quality leads to more effective selection in breeding programs and segregation of more uniform parcels of grain better suited to the needs of customers. Their effects on wheat quality were reviewed using papers obtained from 4 major international databases. The literature is dominated by research from North America, with lesser contributions from Europe, Australia, and the rest of the world. Use of analysis of variance to partition sources of variation due to G, E, and G × E was the most common approach but, more recently, residual maximum likelihood methods that can accommodate large, but unbalanced, datasets have been used. In North America and Europe, the relative contributions of G, E, and G × E varied across studies, but traits associated with protein content were more influenced by E and G × E than those associated with protein quality, dough rheology and starch characteristics, where G effects were more important. Variation in the relative contributions of G, E, and G × E was highly dependent on the G and E sampled. The Australian studies were characterised by a relative lack of G × E, with G and E rankings being similar across the country for the protein quality, dough rheology, and starch quality traits examined in detail. This suggests that, in Australia, more efficient testing of potential cultivars will be possible for these traits, especially when the underlying variation at the gene level is known, and that efficiencies in the design and conduct of trial systems and quality evaluations could be achieved by testing samples from targetted environments without affecting genetic gain and overall crop quality.