Plant Protein Analysis

Abstract

The influx of data from the past ten years of large-scale plant genomes sequencing projects have yielded the sequence, complete or in its final assembly level, of several plant genomes, including Arabidopsis thaliana, Oryza sativa, Zea mays , Brachypodium distachyon, Cucumis sativus, Populus trichocarpa, Medicago truncatula, Glycine max, Malus domestica, Physcomitella patens, Selaginella moellendorfii, Sorghum bicolour, Theobroma cacao, Vitis vinifera, Prunus pumice, Rricinus communis and Vigna radicata. This knowledge, combined with the implementation of classical and innovative parallel high-throughput proteomic technologies associated to new protein search algorithms, has triggered a growing interest in plant proteomics to address a comprehensive analysis of cellular functions from the level of the plant to the whole organisms in different physiological and environmental conditions. A number of reviews have been recently written providing detailed insights into the basic lines of plant proteomics studies (Baginsky, 2009; Rose et al. 2004). In addition a number of initiatives such as the International Plant Proteomics Organization (INPPO) and The Plant Proteomics Database (PPDB) have been launched recently to organize the massive amount of information that emerged within the field of plant proteomics (Agrawal et al. 2011, Sun et al. 2009). Figure 1 highlights the rapid increase of scientific interest in plant proteomics that has occurred in the last ten years with model species including Arabidopsis (Van Norman & Benfey, 2009) and rice (Agrawal & Rakwal, 2011) which opened the way also for studying non-model plants species. The majority of plant proteomics studies to date can be divided into two basic categories: the first involves protein annotation and profiling with the aim of separating and cataloguing as many proteins extracted from whole cells and organelles as possible to provide a snapshot of the major constituents of the proteome. The most notable examples of descriptive plant proteomics are studies carried out in different organs of Arabidopsis (Giavalisco et al. 2005, Baerenfaller et al. 2008, Joshi et al. 2011) and in rice (Agrawal et al. 2009, Koller et al.2002, Ferrari et al. 2011) where, respectively, 13,029 and 2,528 unique proteins have been identified from several tissues. However it should be noted that entire proteomes of single cell types cannot yet be fully mapped, as will be explained later, and to date the number of protein entries in the UniprotKB database for plant organisms is still limited to just above 500,000 which corresponds to less than 1/10th of the total number of entries (Schneider et al. 2009). The second category of proteome analysis aims at revealing