Reconstruction of protein networks from an atlas of maize seed proteotypes

Abstract

A comprehensive knowledge of proteomic states is essential for understanding biological systems. Using mass spectrometry, we mapped an atlas of developing maize seed proteotypes comprising 14,165 proteins and 18,405 phosphopeptides (from 4,511 proteins), quantified across eight tissues. We found that many of the most abundant proteins are not associated with detectable levels of their mRNAs, and we provide evidence for three potential explanations: transport of proteins between tissues; diurnal, outof-phase accumulation of mRNAs and cognate proteins; and differential lifetimes of mRNAs compared with proteins. Likewise, many of the most abundant mRNAs were not associated with detectable levels of their proteins. Across the entire dataset, protein abundance was poorly correlated with mRNA levels and was largely independent of phosphorylation status. Comparisons between proteotypes revealed the quantitative contribution of specific proteins and phosphorylation events to the spatially and temporally regulated starch and oil biosynthetic pathways. Reconstruction of signaling networks established associations of proteins and phosphoproteins with distinct biological processes acting during seed development. Additionally, a protein kinase substrate network was reconstructed, enabling the identification of 762 potential substrates of specific protein kinases. Finally, examination of 694 transcription factors revealed remarkable constraints on patterns of expression and phosphorylation within transcription factor families. These results provide a resource for understanding seed development in a crop that is the foundation of modern agriculture.quantitative proteomics | protein phosphorylation | systems biology A central goal of biology is to understand phenotype. Proteins make or regulate every component of cells, and therefore phenotype is an emergent property of the specific state of the proteome. The proteomic state of a cell is its proteotype, which integrates the constraints of its genotype, developmental history, and environment. Thus, a complete description of the proteotype should define a phenotype at the molecular level. Typically, measurements of mRNA abundance are used to infer the proteotype (1, 2). However, it has become clear that mRNA levels are poorly correlated with protein abundance (3-8). Proteomewide surveys are crucial for bridging this gap and defining specific cellular proteotypes.Maize is a model organism with a rich history in fundamental research in addition to being the world's largest production crop. The maize seed is a developmentally complex structure comprised of two major compartments, the diploid embryo and the triploid endosperm, that arise from two separate fertilization events (double fertilization) and are enclosed within the maternally derived pericarp (9). Like in other grasses, the maize endosperm is persistent throughout seed development (10). The endosperm consists primarily of starchy endosperm cells that are responsible for synthesis of starch and storage proteins and its peri...

Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm

“…This major effect on PPDK level confirms that pdk2-DsEx4 is a loss-of-function allele. The result further indicates that pdk1 conditions a minor portion of the endosperm enzyme, consistent with proteomic data showing PPDK1 to be 5% of the total (22) and enzyme activity data that follows. Loss of pdk1 function had no obvious effect on endosperm PPDK level, consistent with each form's abundance indicated from proteomic analysis.…”

“…This genetic analysis confirms proteomics data (22,32) showing that the great majority of PPDK is specified by pdk2 in endosperm and pdk1 in leaf. The pdk1 and pdk2 products in endosperm are redundant with respect to maintenance of vitreous endosperm character.…”

“…Potential glycolytic function of PPDK in plants is suggested by its markedly increased expression in rice coleoptiles or seedlings subjected to anoxia (18,19). Maize endosperm is another oxygen-limited tissue with high PPDK levels (20)(21)(22), coincident with biomass accumulation and associated ATP demand. Direct evidence of PPDK…”

Transcript, protein and metabolite temporal dynamics in the CAM plant Agave

“…Therefore, we explored the temporal relationships of the expression of each transcript and its encoded protein in Agave. When looking at relationships for a single time point, we observed non-linear relationships with weak correlations (average Pearson's correlation between log-transformed abundances was r = 0.48), which is consistent with results of previous studies 44 . The temporal dynamics between the expression of transcripts and their encoded proteins could explain this variation, which results from various rates of biosynthesis and degradation and subsequent post-transcriptional or -translational modifications.…”

A review of starch‐branching enzymes and their role in amylopectin biosynthesis

“…Recent studies with maize SBEIIb, the major isoform of SBEII in the starch-storing endosperm, have shown that the enzyme can be phosphorylated at three Ser sites by two plastidial Ca 21 -dependent protein kinase (CDPK) activities (14,70). Two of the phosphorylation sites (Ser 286 and Ser 297 ) are highly conserved among the SBEII class (see Fig.…”