Arabidopsis thaliana root cell wall proteomics: Increasing the proteome coverage using a combinatorial peptide ligand library and description of unexpected Hyp in peroxidase amino acid sequences

Abstract

Plant cell walls (CWs) contain a large proportion of polysaccharides (90-95% of CW mass) and proteins (5-10%) that play major roles in CW plasticity during development and in response to environmental cues. Here, we present CW proteomics data of Arabidopsis thaliana roots. Plants were cultivated in hydroponic conditions. CW protein (CWP) extracts were prepared and analyzed in two different ways in order to enlarge the coverage of the root CW proteome: proteins were analyzed either directly or following an affinity chromatography on a combinatorial peptide ligand library (CPLL) to reduce the concentration dynamic range. Proteins were identified by LC-MS/MS and bioinformatics. Altogether, 424 proteins having predicted signal peptides have been identified (CWPs). CPLL permitted to identify low-abundant CWPs never described before, thus enlarging the coverage of the root CW proteome. The number of oxidoreductases is particularly high and includes a large collection of class III peroxidases (CIII Prxs; 38 out of the 73 A. thaliana CIII Prxs). For the first time, hydroxyproline residues were localized at conserved positions in CIII Prx amino acid sequences.

Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates

“…While some of the apoplastic proteins are normally classified as intracellular proteins, such as Varicose (AT3G13300) or NADP-malic enzyme 2 (AT5G11670), they have recently been found in extracellular/cell wall or plasma membrane proteomes (De Michele et al, 2016; Nguyen-Kim et al, 2016). In particular, these also include six members of the Histone 2A family (Table 1), which are typically part of the core nucleosomes (Mitra et al, 2009; Heard et al, 2015; Nguyen-Kim et al, 2016). However, other histones such as Histone 4 have previously also been reported in pea root cap secretome (Wen et al, 2007), suggesting possible extracellular functions of histones.…”

“…a The PubMed ID (PMID) of the publication reporting the plasma membrane (PM), extracellular or plastid proteomics data are indicated: Nguyen-Kim et al, 2016 (PMID:26572690); Mitra et al, 2009 (PMID:19334764); Heard et al, 2015 (PMID:25900983); De Michele et al, 2016 (PMID:26781341); Charmont et al, 2005 (PMID:15694452); Zhang and Peck, 2011 (PMID:21433285); Helm et al, 2014 (PMID:24361574); Melonek et al, 2016 (PMID:26987276) .…”

Understanding the Remodelling of Cell Walls during Brachypodium distachyon Grain Development through a Sub-Cellular Quantitative Proteomic Approach

“…It represented almost a quarter of the total number of CWPs, a proportion which has been found in the cell wall proteomes of various organs of B. distachyon , A. thaliana and O. sativa [15,32,33,34,35]. GHs, expansins, CEs and PNGases were the most represented protein families in the cell wall proteomes of the B. distachyon grain.…”

An enlarged cell wall proteome of Arabidopsis thaliana rosettes

“…The comparison of the rosette cell wall proteome to those of other A. thaliana organs has shown that 219 CWPs were common with that of roots [21][22][23], 64 to that of stems [24] and 135 to that of etiolated hypocotyls [11,12,25]. Besides, 109 CWPs were common to the cell wall proteomes of rosettes and cell suspension cultures [26][27][28][29][30][31] (Table 1).…”