Plant cell wall proteomics: the leadership of Arabidopsis thaliana

Abstract

Plant cell wall proteins (CWPs) progressively emerged as crucial components of cell walls although present in minor amounts. Cell wall polysaccharides such as pectins, hemicelluloses, and cellulose represent more than 90% of primary cell wall mass, whereas hemicelluloses, cellulose, and lignins are the main components of lignified secondary walls. All these polymers provide mechanical properties to cell walls, participate in cell shape and prevent water loss in aerial organs. However, cell walls need to be modified and customized during plant development and in response to environmental cues, thus contributing to plant adaptation. CWPs play essential roles in all these physiological processes and particularly in the dynamics of cell walls, which requires organization and rearrangements of polysaccharides as well as cell-to-cell communication. In the last 10 years, plant cell wall proteomics has greatly contributed to a wider knowledge of CWPs. This update will deal with (i) a survey of plant cell wall proteomics studies with a focus on Arabidopsis thaliana; (ii) the main protein families identified and the still missing peptides; (iii) the persistent issue of the non-canonical CWPs; (iv) the present challenges to overcome technological bottlenecks; and (v) the perspectives beyond cell wall proteomics to understand CWP functions.

Keywords: Arabidopsis thaliana; cell wall; mass spectrometry; peptidomics; proteomics.

Figure 1

Occurrence of cell wall proteomics papers since 1997. The number of papers published each year is represented with colored bars for each plant: A. thaliana (green), O. sativa (pink), P. deltoides (yellow), S. lycopersicum (red), and others (blue). The arrows show the year of the genomic sequence release for each of them. Note that the genomic sequence of P. trichocarpa was used for protein identification in P. deltoides.

Figure 2

Synopsis of the different strategies used for the study of cell wall proteomes and secretomes. Five main steps have been identified in the published strategies and different combinations of the five steps have been used. Steps 1 and 2 lead to protein extraction. Step 3 consists in protein separation. Steps 4 and 5 lead to protein identification by combining MS or Edman N-terminal sequencing and bioinformatics. In some cases, one step is performed twice or even several times, e.g., steps 2 and 3, by modifying the composition of the buffer used for protein recovery or doing two subsequent steps of protein separation. In other cases, one step can be skipped, like step 2 for the analysis of secreted proteins present in culture medium, or step 3 when proteins are directly analyzed by MS.