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.

Cell growth defect factor 1 is crucial for the plastid import of NADPH:protochlorophyllide oxidoreductase A in Arabidopsis thaliana

“…Isolation of CDF1 was initially achieved by using pPORA as bait and purifying IAPs from detergent-solubilized envelopes via Ni-NTA agarose chromatography. Per se, these results are well compatible with previous proteomics studies identifying CDF1 as an envelope protein (36)(37)(38). Structure predictions for CDF1 underscored the presence of four transmembrane domains indicative of an integral membrane protein.…”

“…Proteomics studies, however, also localized CDF1 to the plastid envelope of higher plants (36)(37)(38). Both mitochondria and chloroplasts are important sites of cell death regulation, and it is therefore attractive to hypothesize a role of CDF1 in cell death regulation and suppose a common link to reactive oxygen species accumulating in both organelle types (35,39).…”

Discovery of a Unique Clp Component, ClpF, in Chloroplasts: A Proposed Binary ClpF-ClpS1 Adaptor Complex Functions in Substrate Recognition and Delivery

“…Biochemical analysis using a specific ClpF antibody confirmed that ClpF is chloroplast-localized, with the majority located in the soluble stromal fraction and the remainder associated with chloroplast membranes ( Figure 1C). We did not find ClpF in isolated chloroplast nucleoid fractions in Arabidopsis (Huang et al, 2013), indicating that its role is unlikely to be involved in DNA repair or plastid gene expression. To assess the spatiotemporal regulation of ClpF abundance, its accumulation was determined in different leaf stages and organs of Arabidopsis plants grown on soil ( Figure 1D).…”

Modified Clp Protease Complex in the ClpP3 Null Mutant and Consequences for Chloroplast Development and Function in Arabidopsis

“…These groups contained closely related proteins that were identified with peptides, most of which also matched to homologs (Friso et al, 2011). Based on our recent reference Arabidopsis chloroplast proteome (Huang et al, 2013), 918 proteins were chloroplast localized, representing 63% of the protein mass in clpp3-1 and 69% in the wild type. This reduced chloroplast mass was due to a 50% reduction in lumenal mass and 26% in thylakoid protein mass (Supplemental Table S4).…”

“…pTAC11 (WHY3) and pTAC17, initially identified in transcriptionally active chromosome (TAC) fractions (Pfalz et al, 2006), were 7-and 3-fold up-regulated in clpp3-1, respectively. In particular, pTAC11, but not pTAC17, is strongly enriched in nucleoids Huang et al, 2013). The function of pTAC17 is unknown, but sequence analysis suggests that it may be involved in DNA repair; importantly, we recently identified it as a candidate substrate for the substrate selector ClpS (K. Nishimura, Y. Asakura, G. Friso, J. Kim, S.H.…”