Fig. 5: Comparison of the transcriptional and translational changes of the 82 nucleus-encoded photosynthesis-related proteins whose protein abundance decreased in 6-d-old ClpD-GFP line #5 seedlings.
a Hierarchical clustering heatmap showing the log2 FC (line #5/WT) of the transcripts, footprints, and TEs of the 82 significantly decreased nucleus-encoded photosynthesis-related proteins identified by comparative proteomic analyses. Genes with a protein FC (line #5/WT) over translation output (represented by footprints) FC (line #5/WT) of less than 1.5-fold are marked in green. Proteins whose P-TPs were detected (cf. Supplementary Data 2) are marked with asterisks. b, c Scatter plot showing the correlation between the FC of transcripts and the FC of footprints (b), and between the FC of footprints and the FC of proteins (c) for these 82 genes (cf. Supplementary Data 9). Pearson’s correlation coefficients (r) are indicated. d Normalized distribution of RNA-seq and Ribo-seq reads over representative photosynthesis-related genes in the WT and ClpD-GFP line #5 plants. The fold change and the associated FDR at the transcript, footprint, and TE levels are shown.
