Dataset Information

The grain protein turnover atlas of hexaploid wheat Triticum aestivum

ABSTRACT: Cellular protein abundance results from the relative rates of protein synthesis and protein degradation. Through combining in vivo stable isotope labelling and in-depth quantitative proteomics, we created a protein turnover atlas of wheat grain proteins during grain development. Our data demonstrate that protein turnover rates for 1447 unique wheat grain protein groups have an apparent spatiotemporal pattern that aids explanation of the 60% of variation in protein abundances that are not attributable to gene expression. Protein synthesis rates of individual proteins vary over 100 fold and degradation rates over 20 fold. Storage proteins have both higher synthesis and degradation rates than the overarching average rates of grain proteins in other functional categories, while those proteins involved in photosynthesis, DNA synthesis and glycolysis, by contrast, are house-keeping proteins that show low synthesis and degradation rates at all times. Approximately 20% of total grain ATP production through respiration is used for grain proteome biogenesis and maintenance, and the grain invests nearly half of this budget in storage protein synthesis alone. Degradation of storage proteins as a class of grain proteins also consumed a significant amount of the total ATP allocated to protein degradation processes. This analysis suggests that 20% of newly synthesized storage proteins are turned over rather than stored suggesting that this process is not energetically optimal. This approach to measure protein turnover rates at the proteome scale shows how different functional categories of grain proteins accumulate, calculates the costs of futile cycling of protein turnover during wheat grain development and identifies the most and the least stable wheat grain proteins.

INSTRUMENT(S): 6550A iFunnel Q-TOF LC/MS

ORGANISM(S): Triticum Aestivum (wheat)

TISSUE(S): Plant Cell, Embryo, Endosperm

SUBMITTER: HUI CAO

LAB HEAD: A.Harvey Millar

PROVIDER: PXD022231 | Pride | 2021-12-21

REPOSITORIES: Pride

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Project description:Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization and turnover rates, on a whole proteome level remains a major challenge in the post-genome era. Quantitative methods for measuring mRNA expression do not reliably predict corresponding protein levels and provide little or no information on other protein properties. Here we describe a combined pulse-labelling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation and turnover rates of endogenously expressed, untagged human proteins in different subcellular compartments. Using quantitative mass spectrometry and SILAC, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualised using specialised software tools developed in PepTracker. Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear and nucleolar compartments. Expression levels of endogenous HeLa proteins varied by up to seven orders of magnitude. The average turnover rate for HeLa proteins was approximately 20 hours. Turnover rate did not correlate with either molecular weight or net charge, but did correlate with abundance, with highly abundant proteins showing longer than average half-lives. Fast turnover proteins had overall a higher frequency of PEST motifs than slow turnover proteins but no general correlation was observed between amino or carboxy terminal amino acid identities and turnover rates. A subset of proteins was identified that exist in pools with different turnover rates depending on their subcellular localization. This strongly correlated with subunits of large, multi-protein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.

Dataset Information

The grain protein turnover atlas of hexaploid wheat Triticum aestivum

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