Plastid Reference Proteomes For Maize and Arabidopsis and Comparative Orthoproteome Analysis

Plastids are essential organelles because they contribute to primary and secondary metabolism and plant signaling networks. A high quality inventory of the plastid proteome is therefore a critical tool in plant research. We present reference plastid proteomes for maize (Zea mays) and Arabidopsis (Arabidopsis thaliana) with respectively 1564 and 1559 proteins. This was based on manual curation of published experimental information, including 156 proteomics studies regarding different subcellular fractions, and new quantitative proteomics experiments on plastid subfractions specifically designed to fill gaps in current knowledge. These plastid proteomes represent an estimated 40% (maize) to 50% (Arabidopsis) of all plastid proteins and can serve as a 'gold standard' because of their low false positive rate. To facilitate direct comparison of these plastid proteomes, identify 'missing' proteins and evaluate species-specific differences, we determined their orthologous relationships. The multi-step strategy to best define these orthologous relationships is explained. Putative plastid locations for orthologs without known subcellular location were inferred based on the robustness of orthology and weighing of experimental evidences, increasing both plastid proteome sizes. Examples that highlight differences and similarities between maize and Arabidopsis, and underscore the quality of the orthology assignments, are discussed.