C4 gene induction during de-etiolation evolved through changes in cis to allow integration with ancestral C3 gene regulatory networks.
C4 photosynthesis has evolved by repurposing enzymes found in C3 plants. Compared with the ancestral C3 state, accumulation of C4 cycle proteins is enhanced. We used de-etiolation of C4 Gynandropsis gynandra and C3 Arabidopsis thaliana to understand this process. C4 gene expression and chloroplast biogenesis in G. gynandra were tightly coordinated. Although C3 and C4 photosynthesis genes showed similar induction patterns, in G. gynandra, C4 genes were more strongly induced than orthologs from A. thaliana. In vivo binding of TGA and homeodomain as well as light-responsive elements such as G- and I-box motifs were associated with the rapid increase in transcripts of C4 genes. Deletion analysis confirmed that regions containing G- and I-boxes were necessary for high expression. The data support a model in which accumulation of transcripts derived from C4 photosynthesis genes in C4 leaves is enhanced because modifications in cis allowed integration into ancestral transcriptional networks.