PRJNA682315
Cross-species GOLDEN2-LIKE TF ChIP-seq reveals dynamic cis-regulatory evolution of a conserved regulator
Chloroplast biogenesis and development is of crucial importance to photosynthesis efficiency and plant yield, and GOLDEN2-LIKE (GLK) transcription factors (TFs) are important regulators of chloroplast biogenesis and development in plants. However, whether and how GLK-regulated chloroplast function differs across plant species, particularly the genome-wide occupancy of GLK proteins in diverse plant species remains largely unexplored. Here we profiled GLK occupancy in five plant species, and compared them for the first time. We found that binding targets of paralogous GLK1 and GLK2 substantially overlap in each species and photosynthetic genes are overrepresented in these overlapped target genes. In addition, GLK binding on photosynthetic genes is highly conserved across species. Conservation score in photosynthesis, tetrapyrrole synthesis and signalling is significantly higher than average. Transcriptome analysis indicated that most photosynthetic genes, including those in chlorophyll biosynthesis and light harvesting, are upregulated by GLK proteins in Arabidopsis and tomato. A subset of TF genes is conservatively bound by GLK proteins and they participate in multiple developmental processes, including flowering time control, leaf senescence, plant longevity, and stress responses, suggesting that GLK proteins might be involved in plant developmental processes apart from photosynthesis. We identified some eudicot-specific and monocot-specific GLK targets, however, monocot GLK genes can still rescue Arabidopsis glk1 glk2 pale green leaf phenotype and ~40% of eudicot-specific GLK targets can be bound by ZmGLK1 in Arabidopsis, suggesting that GLK proteins retained the similar binding potential to their orthologs in other species, especially for the core targets involved in photosynthesis, and sequence variation in regulatory regions was responsible, at least in part, for the differential binding targets. Through the comparison of GLK binding targets in eudicot and monocot species that diverged more than 160 million years ago (Mya), we provided evidence that the core set of orthologous genes is conservatively bound by orthologous TFs during evolution, while the TF binding sites may have evolved independently.