We report an extensive proteome analysis of rice etioplasts, which were highly purified from dark-grown leaves by a novel protocol using Nycodenz density gradient centrifugation. Comparative protein profiling of different cell compartments from leaf tissue demonstrated the purity of the etioplast preparation by the absence of diagnostic marker proteins of other cell compartments. Systematic analysis of the etioplast proteome identified 240 unique proteins that provide new insights into heterotrophic plant metabolism and control of gene expression. They include several new proteins that were not previously known to localize to plastids. The etioplast proteins were compared with proteomes from Arabidopsis chloroplasts and plastid from tobacco Bright Yellow 2 cells. Together with computational structure analyses of proteins without functional annotations, this comparative proteome analysis revealed novel etioplast-specific proteins. These include components of the plastid gene expression machinery such as two RNA helicases, an RNase II-like hydrolytic exonuclease, and a site 2 protease-like metalloprotease all of which were not known previously to localize to the plastid and are indicative for so far unknown regulatory mechanisms of plastid gene expression. All etioplast protein identifications and related data were integrated into a data base that is freely available upon request.
Molecular & Cellular Proteomics 4:1072-1084, 2005.Plastids are plant cell organelles that have essential biosynthetic and metabolic activities. These include photosynthetic carbon fixation and synthesis of amino acids, fatty acids, starch, and secondary metabolites such as pigments. Although plastids lost their autonomy and transferred most of their genes to the nucleus during evolution (1), they have retained a small genome encoding ϳ90 proteins. Different plastid types develop in a tissue-specific manner (for a detailed review on plastid biogenesis, see Ref.2). According to their structure, pigment composition (color), and functional differentiation, plastids are classified as elaioplasts that are found in seed endosperm, chromoplasts in fruits and petals, amyloplasts in roots, etioplasts in dark-grown seedlings, and chloroplasts in photosynthetically active tissues (3). These specialized plastids types are typically the result of a differentiation program that is controlled by the cell and tissue type but also by environmental factors.Perhaps the best understood example of plastid differentiation is the light-dependent conversion of etioplasts into chloroplasts. After exposure of dark-grown seedlings to light etioplasts differentiate into photosynthetically active chloroplasts within a few hours. Chloroplast differentiation is accompanied by the assembly of the thylakoid membrane-localized electron transport system, which requires proteins encoded by genes in both nuclear and chloroplast genomes (4, 5). Although chloroplast differentiation has been investigated in detail for many years, the molecular mechanisms that control the differ...