Plant proteome analysis: A 2006 update

Abstract

This 2006 'Plant Proteomics Update' is a continuation of the two previously published in 'Proteomics' by 2004 (Canovas et al., Proteomics 2004, 4, 285-298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529-5548) and it aims to bring up-to-date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2-DE (specifically IEF-SDS-PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel-free protein separation methods and 'second generation' proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope-coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic stresses, PTMs and Protein interactions. Section 8 summarizes the major pitfalls and challenges of plant proteomics.

Quantitative Proteomics of a ChloroplastSRP54Sorting Mutant and Its Genetic Interactions withCLPC1in Arabidopsis

“…Therefore, to study protein-sorting pathways and the consequences of inactivation of specific sorting components, an integrative approach is needed that can monitor many of the protein homeostasis components as well as other cellular functions in parallel. Gelbased and, in particular, MS-based techniques to determine quantitative differences between proteomes have greatly improved in recent years (Goshe and Smith, 2003;Domon and Aebersold, 2006;Bantscheff et al, 2007), and several of these comparative and quantitative techniques have been used to study plants (for review, see Jorrin et al, 2007;Thelen and Peck, 2007). We present a comparative proteomics approach to address the intrachloroplast sorting and homeostasis network and to determine the cellular response outside of the chloroplast.…”

Plant Defense Responses in Opium Poppy Cell Cultures Revealed by Liquid Chromatography-Tandem Mass Spectrometry Proteomics

“…The use of proteomics to study biological processes in plants has gained momentum, although most applications are focused on model systems that typically do not produce specialized metabolites such as alkaloids (7)(8)(9)(10)(11). Proteome reference maps have been produced for a number of plants systems including cell cultures (12) and root (13) etative tissues in pea (16), and maize endosperm (17).…”

Proteomic Analyses of Cells Isolated by Laser Microdissection

“…Most of the studies published in the plant field concern the proteome of Arabidopsis and rice. The work has focused on profiling organs, tissues, cells, and/or subcellular proteomes (Rossignol et al, 2006;Komatsu et al, 2007;Jorrin et al, 2007;Jamet et al, 2008;Baerenfaller et al, 2008;Jorrin et al, 2009;Agrawal & Rakwal, 2011) and studying developmental processes and responses to biotic (Mehta et al, 2008) and abiotic stresses (Nesatyy & Suter 2008) using differential expression strategies. However, proteomics research results have recently appeared on several non-model herbaceous noncrop species, woody plants, fruit and forest trees (Table 1).…”