Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development

Abstract

We performed large-scale, quantitative analyses of the maize (Zea mays) leaf proteome and phosphoproteome at four developmental stages. Exploiting the developmental gradient of maize leaves, we analyzed protein and phosphoprotein abundance as maize leaves transition from proliferative cell division to differentiation to cell expansion and compared these developing zones to one another and the mature leaf blade. Comparison of the proteomes and phosphoproteomes suggests a key role for posttranslational regulation in developmental transitions. Analysis of proteins with cell wall-and hormone-related functions illustrates the utility of the data set and provides further insight into maize leaf development. We compare phosphorylation sites identified here to those previously identified in Arabidopsis thaliana. We also discuss instances where comparison of phosphorylated and unmodified peptides from a particular protein indicates tissue-specific phosphorylation. For example, comparison of unmodified and phosphorylated forms of PINFORMED1 (PIN1) suggests a tissue-specific difference in phosphorylation, which correlates with changes in PIN1 polarization in epidermal cells during development. Together, our data provide insights into regulatory processes underlying maize leaf development and provide a community resource cataloging the abundance and phosphorylation status of thousands of maize proteins at four leaf developmental stages.

MS23, a master basic helix-loop-helix factor, regulates the specification and development of tapetum in maize

“…As expected from its constitutive RNA expression, MS32 was found in both Stage 8 and 10 anthers and was highly abundant in pollen (Table 1). MS32 is a widely expressed protein detected in leaves (Facette et al, 2013) and transcripts are found in multiple organs ( Fig. S13; https://mpss.danforthcenter.org/ dbs/index.php?SITE=maize_RNAseq).…”

“…The total counts of RNA-seq reads in each gene model are normalized to 10 million reads (TP10M) (Zhai et al, 2015). The relative spectral abundance of each protein analyzed by HPLC-MS/MS was normalized as described by Facette et al (2013). RNA-seq data are from W23 fertile anthers (Zhai et al, 2015).…”

“…Pollen was collected from an actively shedding tassel and immediately stored in liquid nitrogen. Trypsindigested protein samples were analyzed by HPLC-MS/MS as described by Facette et al (2013) using duplicate samples.…”

Cellulose Synthesis and Its Regulation

“…The phosphorylation of CESAs has attracted much attention because of the recent development in phosphoproteomic studies and genetic manipulation of CESAs. Phosphoproteomic studies in Arabidopsis and maize discovered that CESA proteins including CESA1, CESA3, and CESA5 are phosphorylated in conserved residues of the hypervariable region at the N-terminus (Nuhse et al, 2004;Facette et al, 2013). The role of phosphorylation of CESA1 was tested by complementing the rsw1 mutant with mutated forms of CESA1 that prevent or mimic phosphorylation.…”

A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes

“…This technique allowed for the identification of more than 12,000 proteins in a maize leaf developmental time-course experiment (Facette et al, 2013) and a similar number of proteins isolated from developing maize seeds (Walley et al, 2013). These studies provided novel insights into protein accumulation patterns in these maize organs during development, which are instrumental for the better understanding of these biological systems.…”