Construction of Plastid Reference Proteomes for Maize and Arabidopsis and Evaluation of Their Orthologous Relationships; The Concept of Orthoproteomics

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• 作者：Mingshu Huang ; Giulia Friso ; Kenji Nishimura ; Xian Qu ; Paul Dominic B. Olinares ; Wojciech Majeran ; Qi Sun ; Klaas J. van Wijk
• 刊名：Journal of Proteome Research
• 出版年：2013
• 出版时间：January 4, 2013
• 年：2013
• 卷：12
• 期：1
• 页码：491-504
• 全文大小：526K
• 年卷期：v.12,no.1(January 4, 2013)
• ISSN：1535-3907

文摘

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 >150 proteomics studies regarding different (sub)cellular 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 鈥済old standard鈥?because of their low false-positive rate. To facilitate direct comparison of these plastid proteomes, identify 鈥渕issing鈥?proteins, and evaluate species-specific differences, we determined their orthologous relationships. The multistep strategy to best define these orthologous relationships is explained. Putative plastid locations for orthologs without known subcellular locations were inferred based on the robustness of orthology and weighing of experimental evidence, 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.

Keywords:

plastid; chloroplast; maize; Arabidopsis; orthoproteome; quantitative proteomics