ORCID Profile
0000-0002-4317-2027
Current Organisation
Edith Cowan University
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Proteomics and Intermolecular Interactions (excl. Medical Proteomics) | Agricultural Biotechnology not elsewhere classified | Crop and Pasture Production | Crop and Pasture Biochemistry and Physiology
Expanding Knowledge in the Agricultural and Veterinary Sciences | Expanding Knowledge in the Biological Sciences | Wheat |
Publisher: Cold Spring Harbor Laboratory
Date: 14-09-2020
DOI: 10.1101/2020.09.14.295733
Abstract: Wheat-rye 1RS.1BL translocation has a significant impact on wheat yield and hence food production globally. However, the genomic basis of its contributions to wheat improvement is undetermined. Here, we generated a high-quality assembly of 1RS.1BL translocation comprising 748,715,293 bp with 4,996 predicted protein-coding genes. We found the size of 1RS is larger than 1BS with the active centromere domains shifted to the 1RS side instead of the 1BL side in Aikang58 (AK58). The gene alignment showed excellent synteny with 1BS from wheat and genes from 1RS were expressed well in wheat especially for 1RS where expression was higher than that of 1BS for the grain-20DPA stage associated with greater grain weight and negative flour quality attributes. A formin-like-domain protein FH14 ( TraesAK58CH1B01G010700 ) was important in regulating cell ision. Two PPR genes were most likely the genes for the multi fertility restoration locus Rf multi . Our data not only provide the high-resolution structure and gene complement for the 1RS.1BL translocation, but also defined targets for enhancing grain yield, biotic and abiotic stress, and fertility restoration in wheat.
Publisher: Elsevier BV
Date: 03-2019
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-08-2018
Abstract: We present a comprehensive analysis of variation in genes and gene expression of allergens and immunoresponsive proteins in wheat.
Publisher: Elsevier BV
Date: 06-2021
Publisher: Public Library of Science (PLoS)
Date: 10-01-2018
Publisher: Frontiers Media SA
Date: 09-09-2021
Abstract: Lysine is the most limiting essential amino acid in cereals, and efforts have been made over the decades to improve the nutritional quality of these grains by limiting storage protein accumulation and increasing lysine content, while maintaining desired agronomic traits. The single lys3 mutation in barley has been shown to significantly increase lysine content but also reduces grain size. Herein, the regulatory effect of the lys3 mutation that controls storage protein accumulation as well as a plethora of critically important processes in cereal seeds was investigated in double mutant barley lines. This was enabled through the generation of three hordein double-mutants by inter-crossing three single hordein mutants, that had all been backcrossed three times to the malting barley cultivar Sloop. Proteome abundance measurements were integrated with their phenotype measurements proteins were mapped to chromosomal locations and to their corresponding functional classes. These models enabled the prediction of previously unknown points of crosstalk that connect the impact of lys3 mutations to other signalling pathways. In combination, these results provide an improved understanding of how the mutation at the lys3 locus remodels cellular functions and impact phenotype that can be used in selective breeding to generate favourable agronomic traits.
Publisher: MDPI AG
Date: 03-11-2021
Abstract: In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.
Publisher: Springer International Publishing
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 04-01-2017
DOI: 10.1038/SREP39876
Abstract: Brachypodium distachyon, a small annual grass with seed storage globulins as primary protein reserves was used in our study to analyse the toxic nature of non-prolamin seed storage proteins related to celiac disease. The main storage proteins of B. distachyon are the 7S globulin type proteins and the 11S, 12S seed storage globulins similar to oat and rice. Immunoblot analyses using serum s les from celiac disease patients were carried out followed by the identification of immune-responsive proteins using mass spectrometry. Serum s les from celiac patients on a gluten-free diet, from patients with Crohn’s disease and healthy subjects, were used as controls. The identified proteins with intense serum-IgA reactivity belong to the 7S and 11–12S seed globulin family. Structure prediction and epitope predictions analyses confirmed the presence of celiac disease-related linear B cell epitope homologs and the presence of peptide regions with strong HLA-DQ8 and DQ2 binding capabilities. These results highlight that both MHC-II presentation and B cell response may be developed not only to prolamins but also to seed storage globulins. This is the first study of the non-prolamin type seed storage proteins of Brachypodium from the aspect of the celiac disease.
Publisher: John Wiley & Sons, Ltd
Date: 16-01-2014
Publisher: Canadian Science Publishing
Date: 10-2005
DOI: 10.1139/G05-042
Abstract: A novel storage protein gene with obvious wheat chimeric structure was isolated from an immature kernel-specific cDNA library prepared from the old Hungarian variety, Bánkúti 1201. This clone contains γ-gliadin sequences in the 5′ region and LMW-glutenin sequences on the 3′ end. A frameshift mutation was also introduced by the putative recombination event. Hence, the amino acid sequence of the C-terminal region was transformed to a completely new polypeptide. Based on this finding, 7 additional recombinant prolamin genes of similar structure were isolated with specific PCR primers. The 8 chimeric clones seem to be derived from 4 in idual γ-gliadin and 3 LMW-glutenin sequences. These genes show remarkable ersity in size, gliadin:glutenin ratio, frameshift mutations, and sulphur content. The putative functional characteristics of the chimeric polypeptides and problems related to the origin of the encoding genes are discussed.Key words: prolamin, chimeric genes, recombination, wheat cDNA library.
Publisher: Cambridge University Press (CUP)
Date: 03-2009
DOI: 10.1017/S0960258508187815
Abstract: Aerosol smoke and smoke-water can break dormancy and promote seed germination of many plant species. In this study we investigated changes in gene expression after imbibition of light-sensitive Lactuca sativa L. cv. ‘Grand Rapids’ achenes with dilute smoke-water compared to water control s les kept in the dark or continuous light, using the fluorescent differential display technique. Although no difference was detected in the smoke-water versus water control s les germinated in light, smoke-water treatment resulted in the differential display of several expressed sequence tags (ESTs) when compared to water control s les kept in the dark. The most pronounced fragments isolated correspond to known genes related to germination, with functions in cell wall expansion, regulation of translation, the cell ision cycle, carbohydrate metabolism and abscisic acid (ABA) regulation. Real-time polymerase chain reaction (PCR) validation revealed that the transcript abundance of the genes, HVA22 , short-chain dehydrogenase/reductase and late embryogenesis abundant protein, are upregulated after smoke treatment when compared to control achenes kept in the light. The results indicate that smoke has a dual effect. On the one hand, the smoke can induce genes that may be linked to ABA action, whereas, on the other hand, it elicits a faster germination rate by inducing a similar pattern in gene expression as light treatment. Smoke effects could be manifested mainly through the induction of the cell ision cycle, cell wall extension and storage mobilization.
Publisher: Springer Science and Business Media LLC
Date: 11-2012
DOI: 10.1007/S10142-012-0302-3
Abstract: Wheat-related disorders are well-studied health problems. Knowledge of the composition and amounts of epitopes present in a single wheat s le represents a significant gap, and the detailed wheat proteome datasets now available can provide the necessary information to carry out an estimation of allergen prediction for a single cultivar. The combined use of genome sequence and allergen databases, prediction methodology, and cereal chemistry results in better understanding of the level of toxicity present in the end-products produced from wheat flour. The workflow presented in this review provides information about the number and distribution of epitopes at single protein, or protein fraction, levels. In addition, epitopes present in the highest frequency and harmful proteins expressed in the highest amount can be identified. The "epitope toxicity" value obtained in this way is a significant research output from the analysis of large datasets that can be applied to the food industry.
Publisher: Frontiers Media SA
Date: 11-08-2021
Abstract: Gluten related disorders, such as coeliac disease, wheat allergy and baker's asthma are triggered by proteins present in food products made from wheat and related cereal species. The only treatment of these medical illnesses is a strict gluten-free diet however, gluten-free products that are currently available in the market can have lower nutritional quality and are more expensive than traditional gluten containing cereal products. These constraints have led to the development of gluten-free or gluten-reduced ingredients. In this vein, a non-GMO wheat flour that purports to contain “65% less allergenic gluten” was recently brought to market. The present study aims to understand the alteration of the proteome profile of this wheat flour material. Liquid chromatography-mass spectrometry was used to investigate the proteome profile of the novel wheat flour, which was contrasted to a wheat flour control. Using both trypsin and chymotrypsin digests and a combined database search, 564 unique proteins were identified with 99% confidence. These proteins and the specific peptides used to identify them were mapped to the wheat genome to reveal the associated chromosomal regions in the novel wheat flour and the mixed wheat control. Of note, several ω- and γ-gliadins, and low-molecular weight glutenins mapping to the short arm of chromosome 1, as well as α-gliadins from the chromosome 6 short arm were absent or expressed at lower levels in the novel wheat variety. In contrast, the high-molecular weight glutenins and α-amylase/trypsin inhibitors were notably more abundant in this variety. A targeted quantitation experiment was developed using multiple reaction monitoring assays to quantify 359 tryptic and chymotryptic peptides from gluten and related allergenic proteins revealing a 33% decrease of gluten protein content in the novel wheat flour s le in comparison to mixed wheat control. However, additional mapping of known allergenic epitopes showed the presence of 53% higher allergenic peptides. Overall, the current study highlights the importance of proteomic analyses especially when complemented by sequence analysis and epitope mapping for monitoring immunostimulatory proteins.
Publisher: Springer Science and Business Media LLC
Date: 08-2012
Publisher: Frontiers Media SA
Date: 10-08-2022
Abstract: Wheat is a major source of nutrition, though in susceptible people it can elicit inappropriate immune responses. Wheat allergy and non-celiac wheat sensitivity are caused by various wheat proteins, including alpha-amylase trypsin inhibitors (ATIs). These proteins, like the gluten proteins which can cause celiac disease, are incompletely digested in the stomach such that immunogenic epitopes reach the lower digestive system where they elicit the undesirable immune response. The only completely effective treatment for these immune reactions is to eliminate the food trigger from the diet, though inadvertent or accidental consumption can still cause debilitating symptoms in susceptible people. One approach used is to prevent the causal proteins from provoking an immune reaction by enhancing their digestion using digestive protease supplements that act in the stomach or intestine, cleaving them to prevent or quench the harmful immune response. In this study, a digestive supplement enriched in caricain, an enzyme naturally present in papaya latex originally designed to act against gluten proteins was assessed for its ability to digest wheat ATIs. The digestion efficiency was quantitatively measured using liquid chromatography-mass spectrometry, including examination of the cleavage sites and the peptide products. The peptide products were measured across a digestion time course under conditions that mimic gastric digestion in vivo , involving the use of pepsin uniquely or in combination with the supplement to test for additive effects. The detection of erse cleavage sites in the caricain supplement-treated s les suggests the presence of several proteolytic enzymes that act synergistically. Caricain showed rapid action in vitro against known immunogenic ATIs, indicating its utility for digestion of wheat ATIs in the upper digestive tract.
Publisher: Elsevier BV
Date: 05-2020
Publisher: Wiley
Date: 09-2003
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/CP18273
Abstract: The wheat NAM-B1 and NAM-A1 genes are positively associated with grain protein content (GPC) in wheat. We conducted molecular characterisation of the NAM-1 genes in 51 Australian wheat varieties (Triticum aestivum L.), with the aim of improving GPC and nitrogen-usage efficiency in Australian wheat. In summary, the wild type NAM-B1 gene, which originated from Israel, was identified in two Australian wheat varieties. Five varieties contained a deletion allele, whereas the majority (43) harboured a non-functional NAM-B1 allele and one variety contained both functional and non-functional alleles. Twenty-six Australian wheat varieties contained the NAM-A1a haplotype, which was similar to its well-characterised homoeolog NAM-B1 wild type and associated with high GPC. The NAM-D1 gene in the 51 wheat varieties was also characterised, and no gene variation in the exon regions was noted only two single-nucleotide polymorphisms in introns 1 and 2 were found among the 51 varieties.
Publisher: Elsevier BV
Date: 08-2019
Publisher: Springer Science and Business Media LLC
Date: 17-08-2018
Publisher: American Chemical Society (ACS)
Date: 15-09-2023
Publisher: Elsevier BV
Date: 08-2021
Publisher: Springer Science and Business Media LLC
Date: 11-2202
DOI: 10.1186/S12870-020-2259-Z
Abstract: 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. 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 in idual 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 in idual 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. 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.
Publisher: Springer Science and Business Media LLC
Date: 17-07-2020
Publisher: Frontiers Media SA
Date: 30-09-2020
Publisher: Springer Science and Business Media LLC
Date: 13-01-2009
DOI: 10.1007/S10142-008-0105-8
Abstract: Smoke from burning vegetation is widely recognised as a germination cue for seed germination and recent reports suggest that smoke treatments can improve seedling vigour also. We investigated the effect of smoke-water on seedling vigour and changes of the global transcriptome in the early post-germination phase in maize. Application of smoke-water improved the germination characteristics and seedling vigour. The transcriptional response of embryos and emerging radicles 24 and 48 h after the onset of smoke treatment was investigated. The microarray study revealed a number of smoke-responsive genes amongst which stress- and abscisic acid (ABA)-related genes were over-represented. The global promoter analysis of the smoke-responsive genes revealed a tight correlation with the results obtained from Gene Ontology annotations. This concerted over-expression shows that smoke treatment induces stress and ABA-related responses in the early post-germination phase which leads to better adaptation to environmental stress factors occurring during germination, eventually resulting in greater seedling vigour.
Publisher: Springer US
Date: 30-11-2012
Publisher: Akademiai Kiado Zrt.
Date: 12-2000
Abstract: Acta Agronomica Hungarica, 48(3), pp. 227–236 (2000) OCCURRENCE OF THE 1RS/1BL WHEAT–RYE TRANSLOCATION IN HUNGARIAN WHEAT VARIETIES B. K Ő SZEGI, G. LINC, A. JUHÁSZ, L. LÁNG and M. MOLNÁR-LÁNG AGRICULTURAL RESEARCH INSTITUTE OF THE HUNGARIAN ACADEMY OF SCIENCES, MARTONVÁSÁR, HUNGARY Received: August 15, 2000 accepted: October 15, 2000 The translocation which involves the substitution of the short arm of the 1R rye chromosome for the short arm of the 1B wheat chromosome by means of centric fusion has exercised an enormous influence on the world’s wheat breeding. Since the first mention of this translocation in 1937 the incidence of the 1RS/1BL translocation has been reported in connection with several hundred wheat varieties. Varieties carrying the translocation possess a chromosome segment which includes the resistance genes Sr31 (stem rust, Puccinia graminis), Lr26 (leaf rust, P. recondita), Yr9 (yellow rust, P. striiformis), Pm8 (powdery mildew, Erysiphe graminis) and Gb (aphid, Schizaphis graminum). The present paper investigates the occurrence of the 1RS/1BL translocation in wheat varieties bred in Hungary in recent years. It was found that 35 (53%) of the 66 Hungarian-bred wheat varieties registered in Hungary between 1978 and 1999 carried the 1RS/1BL translocation.
Publisher: American Chemical Society (ACS)
Date: 08-04-2020
DOI: 10.1021/ACS.JPROTEOME.0C00059
Abstract: α-Amylase/trypsin inhibitors (ATIs) may have a role in nonceliac wheat sensitivity (NCWS) and celiac disease (CD), but the ATI content and ersity across a range of wheat cultivars are not well characterized. Discovery proteomics was used to detect ATIs across two wheat cultivars: Chara and Magenta. Comprehensive mapping of detected ATIs with the ATIs from the recently published wheat genome RefSeq v1.0 shows the presence of three major subclasses: monomeric (9%), dimeric (61%), and chloroform-methanol (CM) type (30%). Subsequently, the level of 18 ATI isoforms (63 peptides) grouped into four subtypes was monitored across 15 commercial wheat cultivars and the eight parental lines from a multiparent advanced-generation intercross (MAGIC) population using liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS). The ATI content of wheat cultivars Janz, Sunvale, Diamond Bird, and Longreach Scout was significantly lower than that of other wheat cultivars. The MAGIC parental cultivars Baxter and Xiaoyan 54 contain higher levels (∼115% relative to the average wheat ATI content), whereas cultivar Pastor contained the lowest levels (∼87%). Comprehensive sequence analysis, annotation, chromosomal locations, and epitope mapping enabled us to build an LC-MRM-MS method to monitor and quantify the immunostimulatory ATI proteins potentially related to NCWS, autoimmune diseases, and metabolic disorders. This provides an opportunity to select wheat cultivars with significantly lower levels of ATIs.
Publisher: Springer Science and Business Media LLC
Date: 24-09-2018
Publisher: Cold Spring Harbor Laboratory
Date: 09-07-2018
DOI: 10.1101/363465
Abstract: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Using chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Sufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
Publisher: Frontiers Media SA
Date: 15-10-2019
Publisher: Frontiers Media SA
Date: 13-05-2022
Abstract: Lupin seeds have an excellent nutritional profile, including a high proportion of protein and dietary fiber. These qualities make lupin seeds an ideal candidate to help meet the growing global demand for complementary sources of protein. Of consequence to this application, there are nutritional and antinutritional properties assigned to the major lupin seed storage proteins—referred to as α-, β-, δ- and γ-conglutins The variation in the abundance of these protein families can impact the nutritional and bioactive properties of different lupin varieties. Hence, exploring the conglutin protein profiles across a erse range of lupin varieties will yield knowledge that can facilitate the selection of superior genotypes for food applications or lupin crop improvement. To support this knowledge generation, discovery proteomics was applied for the identification of the 16 known conglutin subfamilies from 46 domestic and wild narrow-leafed lupin (NLL) genotypes. Consequently, the ersity of abundance of these proteins was evaluated using liquid chromatography–multiple reaction monitoring-mass spectrometry (LC–MRM-MS). This comparative study revealed a larger variability for the β- and δ-conglutin content across the lines under study. The absence/lower abundance of the β2- to β6-conglutin subfamilies in a subset of the domesticated cultivars led to substantially lower overall levels of the allergenic β-conglutin content in these NLLs, for which the elevation of the other conglutin families were observed. The ersity of the conglutin profiles revealed through this study—and the identification of potential hypoallergenic genotypes—will have great significance for lupin allergic consumers, food manufactures as well as grain breeders through the future development of lupin varieties with higher levels of desirable bioactive proteins and lower allergen content.
Publisher: Elsevier BV
Date: 03-2022
Publisher: Akademiai Kiado Zrt.
Date: 12-2008
Abstract: Differential Display RT-PCR was developed before the genomic era to serve as a tool in hunting for genes. Nowadays, applications using state-of-the-art techniques to obtain more information about the whole transcriptome or the genome have rapidly overtaken DD-RT-PCR. This paper will discuss a few of the major drawbacks and limitations of using this once highly valued method.
Publisher: Frontiers Media SA
Date: 06-10-2016
Publisher: American Chemical Society (ACS)
Date: 20-02-2023
Publisher: Cold Spring Harbor Laboratory
Date: 03-09-2018
DOI: 10.1101/406694
Abstract: Wheat Avenin-like proteins (TaALP) are atypical storage proteins belonging to the Prolamin superfamily. Previous studies on ALPs have focused on the proteins’ positive effects on dough strength, whilst no correlation has been made between TaALPs and the plant immune system. Here, we performed genome-wide characterization of ALP encoding genes in bread wheat. In silico analyses indicated the presence of critical peptides in TaALPs that are active in the plant immune system. Pathogenesis-related nucleotide motifs were also identified in the putative promoter regions of TaALP encoding genes. RT-PCR was performed on TaALP and previously characterised pathogenesis resistance genes in developing wheat caryopses under control and Fusarium graminearum infection conditions. The results showed that TaALP and NMT genes were upregulated upon F. graminearum inoculation. mRNA insitu hybridization showed that TaALP genes were expressed in the embryo, aleurone and sub-aleurone layer cells. Seven TaALP genes were cloned for the expression of recombinant proteins in Escherichia coli , which displayed significant inhibitory function on F. graminearum under anti-fungal tests. In addition, FHB index association analyses showed that allelic variations of two ALP genes on chromosome 7A were significantly correlated with FHB symptoms. Over-expression of an ALP gene on chromosome 7A showed an enhanced resistance to FHB. Yeast two Hybridization results revealed that ALPs have potential proteases inhibiting effect on metacaspases and beta-glucosidases. A vital infection process related pathogen protein, F. graminearum Beta-glucosidase was found to interact with ALPs. Our study is the first to report a class of wheat storage protein or gluten protein with biochemical functions. Due to its abundance in the grain and the important multi-functions, the results obtained in the current study are expected to have a significant impact on wheat research and industry.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 17-08-2018
Abstract: Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Ex les of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science , this issue p. eaar7191 see also p. eaar6089
Publisher: Public Library of Science (PLoS)
Date: 29-12-2011
Publisher: Springer Science and Business Media LLC
Date: 06-02-2018
DOI: 10.1038/S41598-018-20935-8
Abstract: Wheat ( Triticum aestivum ) quality is mainly determined by grain storage protein compositions. Sulphur availability is essential for the biosynthesis of the main wheat storage proteins. In this study, the impact of different sulphur fertilizer regimes on a range of agronomically important traits and associated gene networks was studied. High-performance liquid chromatography was used to analyse the protein compositions of grains grown under four different sulphur treatments. Results revealed that sulphur supplementation had a significant effect on grain yield, harvest index, and storage protein compositions. Consequently, two comparative sulphur fertilizer treatments (0 and 30 kg ha −1 sulphur, with 50 kg ha −1 nitrogen) at seven days post-anthesis were selected for a transcriptomics analysis to screen for differentially expressed genes (DEGs) involved in the regulation of sulphur metabolic pathways. The International Wheat Genome Sequencing Consortium chromosome survey sequence was used as reference. Higher sulphur supply led to one up-regulated DEG and sixty-three down-regulated DEGs. Gene ontology enrichment showed that four down-regulated DEGs were significantly enriched in nitrogen metabolic pathway related annotation, three of which were annotated as glutamine synthetase. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment identified three significantly enriched pathways involved in nitrogen and amino acid metabolism.
Publisher: Frontiers Media SA
Date: 28-07-2021
Abstract: Background: To ensure safe consumption of gluten-free products, there is a need to understand all sources of unintentional contamination with gluten in the food chain. In this study, ryegrass ( Lolium perenne ), a common weed infesting cereal crop, is analysed as a potential source of gluten-like peptide contamination. Materials and Methods: Ten ryegrass cultivars were analysed using shotgun proteomics for the presence of proteins from the prolamin superfamily. A relative quantitative assay was developed to detect ryegrass gluten-like peptides in comparison with those found in 10 common wheat cultivars. Results: A total of 19 protein accessions were found across 10 cultivars of ryegrass for the protein families of PF00234-Tryp_alpha_amyl, PF13016-Gliadin, and PF03157-Glutenin_HMW. Protein and peptide homology searches revealed that gliadin-like peptides were similar to avenin and gamma-gliadin peptides. A total of 20 peptides, characteristic of prolamin superfamily proteins, were selected for liquid chromatography mass spectrometry (LC-MS) with multiple reaction monitoring (MRM). Only two of the monitored peptides were detected with high abundance in wheat, and all others were detected in ryegrass. Glutenin and alpha-amylase/trypsin inhibitor peptides were reported for the first time in ryegrass and were noted to be conserved across the Poaceae family. Conclusion: A suite of gluten-like peptides were identified using proteomics that showed consistent abundance across ryegrass cultivars but were not detected in wheat cultivars. These peptides will be useful for differentiating wheat gluten contamination from ryegrass gluten contamination.
Publisher: Elsevier BV
Date: 2018
DOI: 10.1016/J.JBIOTEC.2017.10.016
Abstract: A Cre-lox based auto-excision strategy has been adapted for barley, capable of cre and selectable marker gene (SMG) removal. The cold inducible wheat promoter called wcs120 was utilised for driving Cre expression. The binary vector was carrying the transgene (uidA) and a so called 'recombination cassette' flanked by the lox sequences. This part included both the recombinase gene and the SMG (bar) under the control of a constitutive promoter. T
Publisher: Wiley
Date: 07-2016
Publisher: Springer Science and Business Media LLC
Date: 18-05-2022
DOI: 10.1038/S41586-022-04732-Y
Abstract: Cultivated oat ( Avena sativa L.) is an allohexaploid (AACCDD, 2 n = 6 x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia 1,2 . Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has h ered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A . sativa and close relatives of its diploid ( Avena longiglumis , AA, 2 n = 14) and tetraploid ( Avena insularis , CCDD, 2 n = 4 x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.
Publisher: American Chemical Society (ACS)
Date: 18-08-2022
Publisher: Springer Science and Business Media LLC
Date: 31-08-2004
DOI: 10.1007/S00122-004-1776-8
Abstract: Increased expression of the high molecular weight glutenin subunit (HMW-GS) Bx7 is associated with improved dough strength of wheat (Triticum aestivum L.) flour. Several cultivars and landraces of widely different genetic backgrounds from around the world have now been found to contain this so-called 'over-expressing' allelic form of the Bx7 subunit encoded by Glu-B1al. Using three methods of identification, SDS-PAGE, RP-HPLC and PCR marker analysis, as well as pedigree information, we have traced the distribution and source of this allele from a Uruguayan landrace, Americano 44D, in the mid-nineteenth century. Results are supported by knowledge of the movement of wheat lines with migrants. All cultivars possessing the Glu-B1al allele can be identified by the following attributes: (1) the elution of the By sub-unit peak before the Dx sub-unit peak by RP-HPLC, (2) high expression levels of Bx7 (>39% Mol% Bx), (3) a 43 bp insertion in the matrix-attachment region (MAR) upstream of the gene promoter relative to Bx7 and an 18 bp nucleotide duplication in the coding region of the gene. Evidence is presented indicating that these 18 and 43 bp sequence insertions are not causal for the high expression levels of Bx7 as they were also found to be present in a small number of hexaploid species, including Chinese Spring, and species expressing Glu-B1ak and Glu-B1a alleles. In addition, these sequence inserts were found in different isolates of the tetraploid wheat, T. turgidum, indicating that these insertion/deletion events occurred prior to hexaploidization.
Publisher: Elsevier BV
Date: 06-2018
DOI: 10.1016/J.VIRUSRES.2018.05.005
Abstract: A previous study showed that a single amino acid difference in the cucumber mosaic virus (CMV) capsid protein (CP) elicits unusual symptoms. The wild-type strain (CMV-R) induces green mosaic symptoms and malformation while the mutant strain (CMV-R3E79R) causes chlorotic lesions on inoculated leaves and strong stunting with necrosis on systemic leaves. Virion preparations of CMV-R and CMV-R3E79R were partially purified from Nicotiana clevelandii A. Gray and analysed by two-dimensional gel electrophoresis. Their separated protein patterns showed remarkable differences at the 50-75 kDa range, both in numbers and intensity of spots, with more protein spots for the mutant CMV. Mass spectrometry analysis demonstrated that the virion preparations contained host proteins identified as ATP synthase alpha and beta subunits as well as small and large Rubisco subunits, respectively. Virus overlay protein binding assay (VOPBA), immunogold electron microscopy and modified ELISA experiments were used to prove the direct interaction between the virus particle and the N. clevelandii ATP synthase F1 motor complex. Protein-protein docking study revealed that the electrostatic change in the mutant CMV can introduce stronger interactions with ATP synthase F1 complex. Based on our findings we suggest that the mutation present in the CP can have a direct effect on the long-distance movement and systemic symptoms. In molecular view the mutant CMV virion can lethally block the rotation of the ATP synthase F1 motor complex which may lead to cell apoptosis, and finally to plant death.
Publisher: Wiley
Date: 12-2010
Publisher: Springer Science and Business Media LLC
Date: 2001
Publisher: Elsevier BV
Date: 10-2023
Publisher: MDPI AG
Date: 12-10-2020
DOI: 10.3390/IJMS21207512
Abstract: The success of seed germination and the successful establishment of seedlings across erse environmental conditions depends on seed vigour, which is of both economic and ecologic importance. The smoke-derived exogenous compound karrikins (KARs) and the endogenous plant hormone strigolactone (SL) are two classes of butanolide-containing molecules that follow highly similar signalling pathways to control erse biological activities in plants. Unravelling the precise mode-of-action of these two classes of molecules in model species has been a key research objective. However, the specific and dynamic expression of biomolecules upon stimulation by these signalling molecules remains largely unknown. Genomic and post-genomic profiling approaches have enabled mining and association studies across the vast genetic ersity and phenotypic plasticity. Here, we review the background of smoke-assisted germination and vigour and the current knowledge of how plants perceive KAR and SL signalling and initiate the crosstalk with the germination-associated hormone pathways. The recent advancement of ‘multi-omics’ applications are discussed in the context of KAR signalling and with relevance to their adoption for superior agronomic trait development. The remaining challenges and future opportunities for integrating multi-omics datasets associated with their application in KAR-dependent seed germination and abiotic stress tolerance are also discussed.
Publisher: Oxford University Press (OUP)
Date: 2015
Publisher: Frontiers Media SA
Date: 10-04-2019
Publisher: Springer Science and Business Media LLC
Date: 18-10-2018
Publisher: Elsevier
Date: 2015
Publisher: American Chemical Society (ACS)
Date: 28-07-2021
Publisher: Proceedings of the National Academy of Sciences
Date: 10-12-2018
Abstract: Fifteen full-length wheat grain avenin-like protein coding genes ( TaALP ) were identified on chromosome arms 7AS, 4AL, and 7DS of bread wheat with each containing five genes. Besides the a- and b-type ALPs, a c type was identified in the current paper. Both a and b types have two subunits, named x and y types. The five genes on each of the three chromosome arms consisted of two x-type genes, two y-type genes, and one c-type gene. The a-type genes were typically of 520 bp in length, whereas the b types were of 850 bp in length, and the c type was of 470 bp in length. The ALP gene transcript levels were significantly up-regulated in Blumeria graminis f. sp. tritici (Bgt) -infected wheat grain caryopsis at early grain filling. Wild emmer wheat [(WEW), Triticum dicoccoides ] populations were focused on in our paper to identify allelic variations of ALP genes and to study the influence of natural selection on certain alleles. Consequently, 25 alleles were identified for TdALP-bx-7AS , 13 alleles were identified for TdALP-ax-7AS , 7 alleles were identified for TdALP-ay-7AS , and 4 alleles were identified for TdALP-ax-4AL . Correlation studies on TdALP gene ersity and ecological stresses suggested that environmental factors contribute to the ALP polymorphism formation in WEW. Many allelic variants of ALPs in the endosperm of WEW are not present in bread wheat and therefore could be utilized in breeding bread wheat varieties for better quality and elite plant defense characteristics.
Publisher: Wiley
Date: 09-2013
Publisher: Springer Science and Business Media LLC
Date: 03-2015
Publisher: Springer Science and Business Media LLC
Date: 16-05-2003
DOI: 10.1007/S00122-003-1292-2
Abstract: Bánkúti 1201, an old Hungarian wheat variety with special quality traits, was analysed to determine the relationships between its storage protein composition and superior quality-attributes for breadmaking. Based on the storage protein composition, the variety appears to have the nature of a population, containing several genotypes with different gluten protein alleles. Using molecular markers, a new mutant x-type HMW glutenin allele was identified, containing an extra cysteine residue and showing a moderate, positive-effect on gluten properties. In lines possessing subunits Bx7+By8 the overexpression of the Bx-type subunit could be detected, resulting in a higher unextractable polymeric protein (UPP) content and increased dough strength. It was found that the presence or absence of subunit Bx7 has an equilibrating effect on the dough extensibility, which is generally characteristic of the Bánkúti 1201 population. The complex good bread-making quality of the variety, which has strong but highly extensible dough, is probably due to the balance between lines which express subunit Bx7 and those which do not.
Publisher: Wiley
Date: 23-10-2018
DOI: 10.1111/TPJ.14096
Abstract: In wheat (Triticum aestivum) grain yield and grain protein content are negatively correlated, making the simultaneous increase of the two traits challenging. Apart from genetic approaches, modification of nitrogen fertilization offers a feasible option to achieve this aim. In this study, a range of traits related to nitrogen-use efficiency in six Australian bread wheat varieties were investigated under different nitrogen treatments using 3-year multisite field trials. Changes in the in idual storage protein composition were detected by high-performance liquid chromatography. Our results indicated that wheat grain yield and grain protein content reacted similarly to nitrogen availability, with grain yield being slightly more sensitive than grain protein content, and that genotype is a vital determinant of grain protein yield. Measurement of the glutamine synthetase activity of flag leaves and developing grains revealed that high nitrogen availability prompted the participation of glutamine in biological processes. In addition, a more significant accumulation of gluten macropolymer was observed under the high-nitrogen treatment from 21 days post-anthesis, and the underlying mechanism was elucidated by a comparative proteomics study. A yeast two-hybrid experiment confirmed this mechanism. The results of this study revealed that peptidyl-prolyl cis-trans isomerase (PPIase) was SUMOylated with the assistance of small ubiquitin-related modifier 1 and that high nitrogen availability facilitated this connection for the subsequent protein polymerization. Additionally, luminal-binding protein 2 in the endoplasmic reticulum played a similar role to PPIase in the aggregation of protein under high-nitrogen conditions.
Publisher: Public Library of Science (PLoS)
Date: 15-10-2018
Publisher: Canadian Science Publishing
Date: 05-2006
DOI: 10.1139/G06-069
Publisher: Springer Science and Business Media LLC
Date: 17-04-2015
DOI: 10.1007/S10142-015-0441-4
Abstract: Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments coupled with cis-regulatory elements enrichment study and cluster analysis can be used to define modular gene programs and regulatory networks. Unfortunately, the high molecular weight glutenin subunits of wheat (Triticum aestivum) are more similar than microarray data alone would allow to distinguish between the three homoeologous gene pairs. However, combining complementary DNA (cDNA) expression libraries with microarray data, a co-expressional network was built that highlighted the hidden differences between these highly similar genes. Duplex clusters of cis-regulatory elements were used to focus the co-expressional network of transcription factors to the putative regulatory network of Glu-1 genes. The focused network helped to identify several transcriptional gene programs in the endosperm. Many of these programs demonstrated a conserved temporal pattern across the studied genotypes however, few others showed variance. Based on this network, transient gene expression assays were performed with mutated promoters to inspect the control of tissue specificity. Results indicated that the interactions of the ABRE│CBF cluster with distal promoter regions may have a dual role in regulation by both recruiting the transcription complex as well as suppressing it in non-endosperm tissue. A putative model of regulation is discussed.
Publisher: Elsevier BV
Date: 02-2021
Publisher: Springer Science and Business Media LLC
Date: 02-11-2010
Abstract: Smoke released from burning vegetation functions as an important environmental signal promoting the germination of many plant species following a fire. It not only promotes the germination of species from fire-prone habitats, but several species from non-fire-prone areas also respond, including some crops. The germination stimulatory activity can largely be attributed to the presence of a highly active butenolide compound, 3-methyl-2 H -furo[2,3- c ]pyran-2-one (referred to as karrikin 1 or KAR 1 ), that has previously been isolated from plant-derived smoke. Several hypotheses have arisen regarding the molecular background of smoke and KAR 1 action. In this paper we demonstrate that although smoke-water and KAR 1 treatment of maize kernels result in a similar physiological response, the gene expression and the protein ubiquitination patterns are quite different. Treatment with smoke-water enhanced the ubiquitination of proteins and activated protein-degradation-related genes. This effect was completely absent from KAR 1 -treated kernels, in which a specific aquaporin gene was distinctly upregulated. Our findings indicate that the array of bioactive compounds present in smoke-water form an environmental signal that may act together in germination stimulation. It is highly possible that the smoke/KAR 1 'signal' is perceived by a receptor that is shared with the signal transduction system implied in perceiving environmental cues (especially stresses and light), or some kind of specialized receptor exists in fire-prone plant species which erged from a more general one present in a common ancestor, and also found in non fire-prone plants allowing for a somewhat weaker but still significant response. Besides their obvious use in agricultural practices, smoke and KAR 1 can be used in studies to gain further insight into the transcriptional changes during germination.
Publisher: Elsevier BV
Date: 10-2022
DOI: 10.1016/J.JPROT.2022.104724
Abstract: Exploration of important insect proteins - including allergens - and proteomes can be limited by protein extraction buffer selection and the complexity of the proteome. Herein, LC-MS/MS-based proteomics experiments were used to assess the protein extraction efficiencies for a suite of extraction buffers and the effect of ingredient processing on proteome and allergen detection. Discovery proteomics revealed that SDS-based buffer yields the maximum number of protein groups from three types of BSF s les. Bioinformatic analysis revealed that buffer composition and ingredient processing could influence allergen detection. Upon applying multi-level filtering criteria, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. A targeted LC-MRM-MS assay was developed for the pan-allergen tropomyosin and used to assess the influence of buffer composition and ingredient processing using peptide abundance measurements. SIGNIFICANCE: We demonstrated that the selection of protein extraction buffer and the processing method could influence protein yield and cross-reactive allergen detection from processed and un-processed black soldier fly (BSF) s les. In total, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. An LC-MRM-MS assay was developed for tropomyosin, indicating the importance of buffer selection and processing conditions to reduce BSF s les' allergenicity.
Start Date: 2021
End Date: 12-2024
Amount: $423,650.00
Funder: Australian Research Council
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