The Puzzle of Protein Location in Plant Proteomics pp. 15-30
Authors: (Elisabeth Jamet, Rafael Pont-Lezica, Surfaces Cellulaires et Signalisation chez les Végétaux, Université de Toulouse, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France)
Abstract: Organelle proteomics allows the characterization of complex proteomes to understand the protein networks which regulate growth and development, as well as adaptation and evolution. Purification of organelles is of paramount importance and diverse protocols are published. Some organelles such as chloroplasts, mitochondria, and the nucleus are surrounded by membranes which facilitate their purification. Others have membranes easily disrupted (vacuoles and peroxisomes), or are complex systems for protein trafficking (endoplasmic reticulum, Golgi, and secretory vesicles). The cell walls present different difficulties since they have no physical limits allowing purification. The purity of the targeted cell compartment is usually evaluated by biochemical and/or immunological methods. Nevertheless, in any sub-cellular proteomic analysis, proteins from a different compartment can be detected and the difficulty is to decide whether it is a contamination, or the unexpected location is real and has a functional significance. Software to predict sub-cellular location of proteins is available. However, since not all the targeting signals are known at present, carefulness in the use of such tools is recommended. Different tactics to solve this puzzle are discussed in this commentary.