Fig. 5: Proteomic enrichment of photosynthetic C. zofingiensis proteins are evolutionarily conserved.

a Diagram heatmap of photosystem protein subunit fold change differences in log₂(WT−Fe+Glc/WT+Fe−Glc). b Volcano plot results of statistical pipeline to isolate proteins that were significantly highest or lowest in the heterotrophy (WT−Fe+Glc). Proteins that are stringently highest-(orange) or lowest-in-heterotrophy (turquoise) are in color. They pass a 5% FDR-adjusted p value cutoff (blue line) and a 0.5 fold change cutoff (red line). Select proteins annotations that either represent photosystems (green text) or highest-in-heterotrophy proteins (red) described in the text. The y-axis value is the log₂ fold change of the highest (positive) or lowest (negative) in heterotrophy to the next highest/lowest photosynthetic condition. The x-axis shows the −log₁₀ maximum p value of all highest/lowest WT−Fe+Glc comparisons from any other condition. c Heatmap of the highly significant highest-and lowest-in-heterotrophy proteins across all experiments. d Heatmaps show the protein abundance of single copy and nuclear-encoded orthologs between C. zofingiensis (left three heatmaps) and A. thaliana (right) where each ortholog is associated with photosynthesis in both species. Rows represent orthologous relationships, where a C. zofingiensis and A. thaliana proteins in the same row are one-to-one orthologs of each other. The A. thaliana heatmap is plotted with all mean time point abundances log₂ normalized to the 0 h timepoint of etiolated cotyledons. Data for A. thaliana are from a de-etiolation experiment (ref. ³⁴) represented by the infographic at the top of the heatmap. All included proteins had log₂ fold change >1 at 96. Where available, manually annotated abbreviations from C. zofingiensis¹¹ are labeled in the middle in orange and Araport11 aliases are labeled in green. The A. thaliana GO slim database (updated 01-01-2021)⁴³ was used to extract which genes had a photosynthetic light harvesting associated GO term (green dot, column on right) and genes that were “inferred from mutant phenotype” (red dot GO evidence code: “IMP”) are also labeled. The bottom set of orthologs lacks both photosynthesis GO and mutational evidence in any condition according to GO slim database. PSI/II (photosystem I/II), Cyt b₆f (cytochrome b₆f), ATPs (plastid ATP synthase), FLD1 (flavodoxin 1), FNR1 (flavodoxin-NADP reductase 1), FDX1 (ferredoxin 1 or PETF). Source data are provided in the Source Data File.