Fig. 3: AUREO1c regulates multiple processes related to photosynthesis and photoprotection, and can bind the promoters of LHCX2 and LHCX3.

a Enriched gene ontology (GO) terms for genes regulated in HWL compared to GL in wild type (WT), separated into AUREO1c-dependent and AUREO1c-independent gene groups (see “Methods” for definitions). These GO terms had an adjusted p value (p. adjust) <0.05. The p values were obtained from the one-sided Fisher’s exact test used in the clusterProfiler package, and Benjamini–Hochberg method was used to adjust for multiple comparisons (see “Methods”). The length of each bar is calculated based on its adjusted p value. b A scatterplot of all the genes in P. tricornutum genome showing their responses to HWL in WT cells and the effect of the aureo1c-1 mutation on their expression. LHC family genes and nuclear genes encoding subunits of the photosynthetic electron transport chain (ETC) are highlighted. The data plotted were averages from three independent cultures. c Genes encoding ETC components color-coded to show relative expression levels. The ratio of the transcript abundance of ETC genes between aureo1c-1 and WT under HWL is shown as a heatmap; red and blue indicate higher and lower expression in aureo1c-1 compared to WT respectively. Many of the ETC subunits are encoded by the chloroplast genome and could not be detected in regular RNA-Seq experiments; these are shown as the gray background for each complex. Association between the light-harvesting complex (LHC) family members with photosystem II or photosystem I has not been entirely elucidated. They are shown as green rods here, with their transcript abundance details in (d). Fld flavodoxin, FNR ferredoxin-NADP⁺ oxidoreductase, PS photosystem, Cyt b₆f cytochrome b₆f complex. Two FLD and four FNR gene isoforms were detected and plotted. The data plotted were averages from three independent cultures. d A heatmap showing the expression levels of the chlorophyll-binding protein-encoding genes in the LHC family. The genes were hierarchically clustered into five major categories (I–V). The expression level for each of the three independent cultures under each condition was plotted separately as a column. e DNA affinity purification sequencing (DAP-Seq) results showing enrichment of promoter regions of LHCX2 and LHCX3 in sequences bound to the AUREO1c protein. Note that different gene model annotations exist for LHCX2, and the Phatr2_54065 model shown in this panel is supported by our RNA-Seq and PCR validation results presented in Supplementary Fig. 16. This experiment was repeated twice independently with consistent results and a representative result is shown. f Electrophoretic mobility shift assays (EMSAs) showing the binding of recombinant AUREO1c to DNA probe harboring sequences from the promoters of LHCX2 and LHCX3 respectively. The competing unlabeled probes were applied in excess, as indicated (50–200x). An upper shift of the labeled probes suggests their binding to the AUREO1c protein. The experiment was repeated three times independently, yielding similar results and a representative result is shown. Source data are provided as a Source Data file.