Proteomics in Deciphering the Auxin Commitment in the Arabidopsis thaliana Root Growth

Abstract

The development of plant root systems is characterized by a high plasticity, made possible by the continual propagation of new meristems. Root architecture is fundamental for overall plant growth, abiotic stress resistance, nutrient uptake, and response to environmental changes. Understanding the function of genes and proteins that control root architecture and stress resistance will contribute to the development of more sustainable systems of intensified crop production. To meet these challenges, proteomics provide the genome-wide scale characterization of protein expression pattern, subcellular localization, post-translational modifications, activity regulation, and molecular interactions. In this review, we describe a variety of proteomic strategies that have been applied to study the proteome of the whole organ and of specific cell types during root development. Each has advantages and limitations, but collectively they are providing important insights into the mechanisms by which auxin structures and patterns the root system and into the interplay between signaling networks, auxin transport and growth. The acquisition of proteomic, transcriptomic, and metabolomic data sets of the root apex on the cell scale has revealed the high spatial complexity of regulatory networks and fosters the use of new powerful proteomic tools for a full understanding of the control of root developmental processes and environmental responses.

Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase, as a Novel Regulator of Root Meristem Maintenance

“…Initial characterization of auxin-responsive proteomes in seedlings and roots identified proteins that are responsive 6–24 h after auxin treatment (10, 11) and protein phosphorylation events associated with auxin-mediated lateral root formation (12). However, further studies of the auxin-regulated proteome are needed to generate a more comprehensive view of auxin-mediated gene expression (13).…”

Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings

“…Additionally, transcriptional changes in Arabidopsis seedlings have been well documented . Initial characterization of auxin responsive proteomes in seedlings and roots identified proteins that are responsive 6–24 h after auxin treatment, but further studies of the auxin‐regulated proteome are needed to generate a more comprehensive view of auxin mediated gene expression …”

“…[3][4][5][7][8][9][10] Initial characterization of auxin responsive proteomes in seedlings and roots identified proteins that are responsive 6-24 h after auxin treatment, [11][12][13] but further studies of the auxin-regulated proteome are needed to generate a more comprehensive view of auxin mediated gene expression. [14] In this study, we characterized the auxin-regulated proteome in Arabidopsis by treating 5-day-old seedlings grown on 0.5× Murashige and Skoog (MS) media overlaid with nylon mesh with 1 µm indole-3-acetic acid (IAA), a naturally occurring auxin ("auxin treated"), or an equivalent volume of 95% ethanol diluted in 0.5× MS ("mock" treated) for 3 h (Figure 1A). Proteins were extracted and processed into peptides, which were iTRAQ 4-plex labeled, pooled, and then identified and quantified using tandem mass spectrometry (MS/MS) ( Figure 1A) according to previously utilized methods.…”

Exogenous Auxin Elicits Changes in the Arabidopsis thaliana Root Proteome in a Time-Dependent Manner

“…The effects of auxin on Arabidopsis root growth at the protein level has been reviewed [ 5 ]. Zhang et al [ 6 ] observed changes in the phosphorylation status of 20 proteins, including SORTING NEXIN 1 (SNX1), after exposure of roots to auxin for 2 h. The additional mutational analysis of serine 16 of SNX1 demonstrated its involvement in lateral root formation.…”