Large-scale comparative phosphoprotein analysis of maize seedling leaves during greening

Abstract

MAIN CONCLUSION : Large-scale comparative phosphoprotein analysis in maize seedlings reveals a complicated molecular regulation mechanism at the phosphoproteomic level during de-etiolation. In the present study we report a phosphoproteomic study conducted on Zea mays etiolated leaves harvested at three time points during greening (etiolated seedlings and seedlings exposed to light for 6 or 12 h). We identified a total of 2483 phosphopeptides containing 2389 unambiguous phosphosites from 1339 proteins. The abundance of nearly 692 phosphorylated peptides containing 783 phosphosites was reproducible and profiled with high confidence among treatments. Comparisons with other large-scale phosphoproteomic studies revealed that 473 of the phosphosites are novel to this study. Of the 783 phosphosites identified, 171, 79, and 138 were identified in 0, 6, and 12 h samples, respectively, which suggest that regulation of phosphorylation plays important roles during maize seedling de-etiolation. Our experimental methods included enrichment of phosphoproteins, allowing the identification of a great number of low abundance proteins, such as transcription factors, protein kinases, and photoreceptors. Most of the identified phosphoproteins were involved in gene transcription, post-transcriptional regulation, or signal transduction, and only a few were involved in photosynthesis and carbon metabolism. It is noteworthy that tyrosine phosphorylation and calcium signaling pathways might play important roles during maize seedling de-etiolation. Taken together, we have elucidated a new level of complexity in light-induced reversible protein phosphorylation during maize seedling de-etiolation.

Analysis of tartary buckwheat ( Fagopyrum tataricum ) seed proteome using offline two‐dimensional liquid chromatography and tandem mass spectrometry

“…The distribution of seed proteins’ subcellular localization varies with different developmental stages, seed structure, etc. In many studies on seed germination, the “nucleus” is the subcellular structure with the most protein species, due to vigorous cell division activity (Ning et al, ; Wang et al, ). Unlike the developing seeds, The TBS samples in this study were dormant seeds in storage.…”

“…The distribution of seed proteins' subcellular localization varies with different developmental stages, seed structure, etc. In many F I G U R E 2 The mass error (a) and length (b) distribution of the identified peptides from buckwheat seeds; sequence coverage (c) and molecular weight (d) distribution of the identified proteins from tartary buckwheat seeds studies on seed germination, the "nucleus" is the subcellular structure with the most protein species, due to vigorous cell division activity (Ning et al, 2016;Wang et al, 2017). Unlike the developing seeds, The TBS samples in this study were dormant seeds in storage.…”

Transcriptome Analyses of Two Citrus Cultivars (Shiranuhi and Huangguogan) in Seedling Etiolation

“…It has been reported that more than 1000 genes are modulated at the transcript level during the greening of Arabidopsis and Rice etiolated seedlings17. There have been so many studies on greening, mainly focused on gene expression, particularly of photosynthetic genes, and on modulation of the corresponding protein levels18. In addition, a proteomic analysis that focused on light-induced development of chloroplasts from etioplasts was also performed on rice seedlings during greening19.…”

Large-scale Proteomic and Phosphoproteomic Analysis of Maize Seedling Leaves During De-etiolation

“…To perform a deep analysis of the maize proteome and phosphoproteome during de-etiolation, the first leaves of etiolated 7-day-old maize seedlings (B73 inbred) were illuminated with white light and harvested at 0 h, 1 h, 6 h and 12 h for mass spectrometry analysis ( Figure 1 ). We chose these samples for analysis because in our previous studies [25, 31, 32] we found that the first leaves of 7-day-old etiolated maize seedlings showed no significant changes in growth compared with light-grown seedlings when subjected to illumination for 12 hours, and few proteins involved in development and growth were found to be differently expressed when comparing the proteomes of etiolated and normal leaves. Moreover, the etiolated leaves turned green after 12 hours of illumination, which indicated that processes related to greening in leaves were completed.…”

“…The completion of the B73 maize genome [26] has facilitated the use of large-scale transcriptome and proteome data to reveal the mechanisms underlying various maize developmental and physiological processes. For example, researchers have created large data resources for C4 photosynthesis research, including complementary RNA-seq [27], proteomics [28, 29], and phosphoproteomics [30, 31] data for a developmental gradient of the maize leaf. In these studies, the mRNA and protein contents at successive stages of photosynthetic development were analyzed.…”