*3.4. Photosynthesis*

In current literature photosynthesis-associated nuclear genes (PhANGs) are referenced as the "classical" target of biogenic retrograde signals [24,35]. Our meta-analysis indicates that PhANGs represent only a part of the gene groups being affected when chloroplast biogenesis is blocked (Figure 1C). Nevertheless, this group appears to be the one exhibiting the highest homogeneity in their mode of expression change among all groups of the module (Figure 2A–G) displaying a very low expression when chloroplast biogenesis is blocked while being highly induced upon etioplast-to-chloroplast conversion (WT-light vs. WT-dark). Interestingly, we identified only genes for components of the photosystem I (PSI) complex and for peripheral parts of photosystem II (PSII) including the light-harvesting antenna and the water splitting complex. Genes for subunits of the ATP-synthase, the Cyt*b6f*-complex and the NAD (P) H-dehydrogenase-like (NDH) complex as well as for enzymes of the Calvin-Benson cycle (with the phosphoribulokinase as only exception) were not identified. This implies a model in which RB signals modulate gene expression of PhANGs in a subset-specific way rather than a common overall control. It appears that especially components of the chlorophyll containing complexes respond to RB signals. Concomitant with this we observed a significant impact of RB signals on genes for key enzymes of Chl and carotenoid biosynthesis suggesting that RB signals may coordinate the syntheses of pigments and pigment-containing complexes.















**Figure 2.** Expression patterns of selected functional groups within the identified core module. Microarray based expression data of light-grown seedlings treated with LIN or NF are given in comparison to wild type (WT LIN vs. WT and WT NF vs. WT, respectively). Expression data from the *pap7-1* mutant are given in comparison to light-grown WT (*pap7-1* vs. WT light), and dark grown WT (*pap7-1* vs. WT dark). As general control expression data of light-grown WT in relation to dark-grown WT are given. All data represent log2-fold expression changes and are supported by colour code indicated in the bottom right corner of figure G. Gene identities (Locus) and respective encoded proteins (Description) are given in columns to the left. Functional groups are indicated on top of each table and are arranged in functionally related subsets. (**A**) Photosynthesis, (**B**) carbohydrate metabolism and transport, (**C**) redox regulation, (**D**) development, (**E**) transcription, (**F**) proteins and stress, (**G**) lipids and hormones. Genes encoding proteins with predicted or proven plastid localization are highlighted in light-green. For details see Supplemental Table S1.
