RT Journal Article
SR Electronic
T1 Finding the LMA needle in the wheat proteome haystack
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.01.22.525108
DO 10.1101/2023.01.22.525108
A1 Delphine Vincent
A1 AnhDuyen Bui
A1 Vilnis Ezernieks
A1 Saleh Shahinfar
A1 Timothy Luke
A1 Doris Ram
A1 Nicholas Rigas
A1 Joe Panozzo
A1 Simone Rochfort
A1 Hans Daetwyler
A1 Matthew Hayden
YR 2023
UL http://biorxiv.org/content/early/2023/01/23/2023.01.22.525108.abstract
AB Late maturity alpha-amylase (LMA) is a wheat genetic defect causing the synthesis of high isoelectric point (pI) 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 (FN) 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’s 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 large-scale high-throughput proteomics experiment along with the challenges associated with big data analyses 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 wellas 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, whereas 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.Competing Interest StatementThe authors have declared no competing interest.