MassIVE MSV000090572

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A community resource to mass explore the wheat grain proteome and its application to the late-maturity alpha-amylase problem.

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Description

Late maturity alpha amylase is a wheat genetic defect causing the synthesis of high isoelectric point alpha amylase in the aleurone as a result of a temperature shock during mid grain development or prolonged cold throughout grain development leading to an unacceptable low falling numbers at harvest or during storage. High pI alpha amylase is normally not synthesized until after maturity in seeds when they may sprout in response to rain or germinate following sowing the next season crop. Whilst the physiology is well understood, the biochemical mechanisms involved in grain LMA response remain unclear. We have employed high throughput proteomics to analyse thousands of wheat flours displaying a range of LMA values. We have applied an array of statistical analyses to select LMA responsive biomarkers and we have mined them using a suite of tools applicable to wheat proteins. To our knowledge, this is not only the first proteomics study tackling the wheat LMA issue but also the largest plant based proteomics study published to date. Logistics, technicalities, requirements, and bottlenecks of such an ambitious experiment are discussed. We observed that stored LMA affected grains activated their primary metabolisms such as glycolysis and gluconeogenesis, TCA cycle, along with DNA and RNA binding mechanisms, as well as protein translation. This logically transitioned to protein folding activities driven by chaperones and protein disulfide isomerase, as well as protein assembly via dimerisation and complexing. The secondary metabolism was also mobilised with the up regulation of phytohormones, chemical and defense responses. LMA further invoked cellular structures among which ribosomes, microtubules, and chromatin. Finally, and unsurprisingly, LMA expression greatly impacted grain starch and other carbohydrates with the up regulation of alpha gliadins and starch metabolism, while LMW glutenin, stachyose, sucrose, UDP galactose and UDP glucose were down regulated. This work demonstrates that proteomics deserves to be part of the wheat LMA molecular toolkit and should be adopted by LMA scientists and breeders in the future. DOI: 10.1093/gigascience/giad084 [doi:10.25345/C53N20J8S] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: bottom-up shotgun proteomics ; late maturity alpha-amylase LMA ; statistics ; data mining

Contact

Principal Investigators:
(in alphabetical order) 		Delphine Vincent, Agriculture Victoria Research, Australia
Submitting User: delphine_1_2
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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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