Fig. 5: Proteome differences reveal a role of Tig2 in chloroplast ribosome biogenesis. | Nature Communications

Fig. 5: Proteome differences reveal a role of Tig2 in chloroplast ribosome biogenesis.

From: A truncated variant of the ribosome-associated trigger factor specifically contributes to plant chloroplast ribosome biogenesis

Fig. 5

Proteomic comparison between Col-0 and tig2 mutant lines. a Experimental setup: Plants were kept for two weeks at 21 °C or transferred to 4 °C for cold acclimation over three weeks. Whole seedlings were harvested and subjected to mass spectrometric analysis. b Direct comparison of protein abundance (given as mean value of log2-transformed LFQ, derived of four biological replicates) between Col-0 and tig2. Pearson’s r and ANOVA p-values are given in the graph. c Left panel: percentage of significantly changed proteins (FDR 0.05 and S0 = 1) between plants grown a room temperature or 4 °C; right panel: number of proteins that are significantly up- or downregulated in the two lines. d, e Volcano plots of the fold-changes plotted against the p-values of Col-0 and the tig2 mutant for plants grown at 21 °C or 4 °C, respectively. The p-values derive from two-sided t-test, a minimal fold change S0 = 1, and a permutation-based FDR < 0.05, with at least three valid values in both groups. f Gene Ontology (GO) enrichment for proteins with significant reduction in tig2 compared to Col-0. For Biological Process, GO IDs are: GO:0009813 for “flavonoid biosynthetic process”, GO:0000302 for "response to reactive oxygen species", GO:0006412 for "translation" and GO:0009628 for “response to abiotic stimulus”. For Cellular Component, GO IDs are: GO:0000311 for “large ribosomal subunit”, GO:0009941 for “chloroplast stroma chloroplast envelope”, GO:0009535 for “chloroplast thylakoid membrane”, GO:0000325 for “plant-type vacuole” and GO:0031410 “cytoplasmic vesicle”. g Box blots of log2 LFQ values of chloroplast ribosomal proteins of the four biological replicates with median shown as solid line, box indicating lower and upper quartile and the whiskers defining data points that fall within 1.5 times the interquartile range (IQR) from the lower and upper quartiles. Data point outside this range is considered as outlier. h Heat map visualizing log2 fold changes between 21 °C and 4 °C grown Col-0 and tig2 lines (left panel) and changes between Col-0 and tig2 (right panel). Proteins which were only detected in one line are shown below the graph. Asterisks indicate proteins with significant changes (two-sided t-test, a minimal fold change S0 = 1, and a permutation-based FDR < 0.05) for the respective condition.

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