Common and Specific Protein Accumulation Patterns in Different Albino/Pale-Green Mutants Reveals Regulon Organization at the Proteome Level  

Abstract

Research interest in proteomics is increasingly shifting toward the reverse genetic characterization of gene function at the proteome level. In plants, several distinct gene defects perturb photosynthetic capacity, resulting in the loss of chlorophyll and an albino or pale-green phenotype. Because photosynthesis is interconnected with the entire plant metabolism and its regulation, all albino plants share common characteristics that are determined by the switch from autotrophic to heterotrophic growth. Reverse genetic characterizations of such plants often cannot distinguish between specific consequences of a gene defect from generic effects in response to perturbations in photosynthetic capacity. Here, we set out to define common and specific features of protein accumulation in three different albino/pale-green plant lines. Using quantitative proteomics, we report a common molecular phenotype that connects the loss of photosynthetic capacity with other chloroplast and cellular functions, such as protein folding and stability, plastid protein import, and the expression of stress-related genes. Surprisingly, we do not find significant differences in the expression of key transcriptional regulators, suggesting that substantial regulation occurs at the posttranscriptional level. We examine the influence of different normalization schemes on the quantitative proteomics data and report all identified proteins along with their fold changes and P values in albino plants in comparison with the wild type. Our analysis provides initial guidance for the distinction between general and specific adaptations of the proteome in photosynthesisimpaired plants.

Characterization of Chloroplast Protein Import without Tic56, a Component of the 1-Megadalton Translocon at the Inner Envelope Membrane of Chloroplasts

“…The TOC components Toc159, Toc132, and Toc75 as well as Tic110 and Tic40 were detected at normal or even higher levels in the mutant plants compared with the wild-type control. Higher TOC/ TIC protein levels were detected also in other albino mutants with defects in genes unrelated to chloroplast protein translocation (Motohashi et al, 2012). Thus, our data suggest that a lack of Tic56 perturbs neither the TOC translocon nor the Tic110-Tic40 complex.…”

Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance

“…5A; Supplemental Table S3). However, reduced ribosomal protein accumulation is not a feature common to all albino/pale green (apg) mutants, because ribosomal subunits accumulate to wild-type levels in the apg1, apg2, and apg3 mutants, which are defective in proteins that participate in diverse chloroplast functions (Motohashi et al, 2012). Because Toc159 is an import receptor for photosynthesis-related proteins, a straightforward explanation for the ppi2 photosynthesis phenotype is that it is caused by a defect in the import of the photosynthesis proteins.…”

Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly

“…To assess in how far the proteomes of both import mutants reflect features of a general albino phenotype as previously reported (Motohashi et al, 2012), we compared the ppm-normalized proteomics data obtained for the two import mutants with those of three albino/pale-green (apg) mutants (Fig. 3).…”

“…The heat map exclusively displays proteins that were identified in all mutant lines and represents a very constrained data set. Including proteins that were not identified in one or several of the albino lines increases the number of commonly regulated proteins, because all albino plants lack, for example, photosynthetic protein accumulation to a different extent Motohashi et al, 2012; Supplemental Table S2). Thus, the data suggest that most of the features of protein accumulation in the two albino import mutants ppi2 and tic56-1 are independent of a function of the two defective proteins in protein import.…”

“…The import mutants ppi2 and tic56-1 accumulate reduced levels of ribosomal proteins. A, The heat map compares the quantitative protein identifications from ppi2 and tic56-1 plastid proteomes with a recently reported albino reference proteome study for three apg1-3 (Motohashi et al, 2012). The data are presented as log 2 ratios between protein quantity in the indicated mutant in comparison to its wild-type control (e.g.…”