title: Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics.
abstract: 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 "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 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.
authors.affiliation: Department of Plant Biology, Cornell University, Ithaca, New York 14853, United States.
authors.forename: Mingshu
authors.initials: M
authors.lastname: Huang
authors.forename: Giulia
authors.initials: G
authors.lastname: Friso
authors.forename: Kenji
authors.initials: K
authors.lastname: Nishimura
authors.forename: Xian
authors.initials: X
authors.lastname: Qu
authors.forename: Paul Dominic B
authors.initials: PD
authors.lastname: Olinares
authors.forename: Wojciech
authors.initials: W
authors.lastname: Majeran
authors.forename: Qi
authors.initials: Q
authors.lastname: Sun
authors.forename: Klaas J
authors.initials: KJ
authors.lastname: van Wijk
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D005069:Evaluation Studies as Topic; D019143:Evolution, Molecular; D018087:Plastids / Q000235:genetics / Q000378:metabolism; D020543:Proteome; D013045:Species Specificity; D003313:Zea mays / Q000235:genetics / Q000378:metabolism
chemical_list: D020543:Proteome