The protein expression landscape of the Arabidopsis root

Abstract

Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.plant proteome | cell-type expression | FACS | RNA-protein correlation | root hair mutant M ulticellular organisms use specialized cell types to perform activities that are integral to their function. Cellular tasks are usually achieved by proteins, which act in signaling cascades, provide structural support, and catalyze enzymatic reactions vital to growth and metabolism. Knowledge of protein cellular localization and abundance using proteomic approaches is thus crucial to our understanding of biological systems (1, 2). Proteome data can be visually represented in a map, which highlights the spatial relationships of proteins at the level of cell type, tissue, or organ. Proteome maps are useful representations of the complex "building plan" of a biological system and also serve as valuable tools for the discovery of new cellular functions (2, 3). Proteomic studies of single cell populations isolated from a variety of multicellular organisms have recently been achieved, including the oocytes of worms and mice (4-6); pollen grains (consisting of two sperm and one vegetative cell) and stomatal guard cells of plants (7,8); and sperm cells of mice and flies (9, 10). These cell types were relatively accessible because they either reside on the surface and can be purified in large quantities using biochemical fractionation (e.g., guard cells) or are large and can easily be collected (e.g., Caenorhabditis elegans oocytes). However, similar proteomic studies of internal cell populations have been more difficult and are usually only partially represented in proteomes of whole organs owing to signal dilution (e.g., refs. 11-16).The Arabidopsis thaliana root is an excellent model for investigating cellular functions internal to an organ because it is transparent, radially symmetric, and cell types can be isolated by FACS to allow molecular profiling (17). The goal of this study was to investigate cell-type function by genera...

Reconstruction of protein networks from an atlas of maize seed proteotypes

“…Specifically, measures of mRNA correlate poorly with protein abundance, which is itself largely independent of phosphorylation status. The lack of correlation between mRNA and protein levels has been documented in other organisms (3)(4)(5)(6)(7)(8). However, we were surprised by the observation that many of the most abundant proteins had little to no measurable mRNA.…”

“…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)(4)(5)(6)(7)(8). Proteomewide surveys are crucial for bridging this gap and defining specific cellular proteotypes.…”

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

“…However, a growing body of research has found only moderate correlation between transcript and protein abundance (Gygi et al, 1999;Schwanhäusser et al, 2011;Petricka et al, 2012;Vogel and Marcotte 2012;Walley et al, 2013;Ponnala et al, 2014). In this study, Pearson and Spearman rank correlation coefficients revealed moderate positive relationships between transcript and protein abundance in primary root tissues (Table II).…”

Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root Apex

“…The data were derived from four individual microarray and proteomic studies in distinctive cell populations of the root (Birnbaum et al, 2003;Brady et al, 2007;Dinneny et al, 2008;Petricka et al, 2012). To compare the cellspecific gene expression of CK-related genes with the CK gradient maps ( Figure 5; Supplemental Figure 6), the data were classified into four categories corresponding to the cell-type populations in which M0028:GFP, J2812:GFP, pWOL:GFP, and pSCR:GFP are expressed.…”