Comparative Network Analysis of C4 Photosynthesis in Grass Species

Transcriptional regulatory networks are complex molecular systems that determine differential gene expression in response to environmental or developmental signals.  Transcriptional regulation relies on the combinatorial interplay of trans-acting protein complexes, and cis-regulatory sequence elements located in or near target genes.  C₄ photosynthesis is an example of a complex metabolic pathway that requires special and temporal expression of specific gene combination for its proper function.  The C₄ pathway coordinates its function between two distinct, specialized leaf cell types, mesophyll (ME) and bundle sheath (BS).  The C₄ pathway has evolved independently in at least 60 lineages of angiosperms, and at least 17 times in the grasses alone.  In the current work, RNA-seq data from three developmental stages of each BS and M cells, were used to analyze transcriptional regulatory networks in three C₄ species, Zea mays, Sorghum bicolor, and Setaria viridis.  These three species represent two independent events of C₄ photosynthesis.  Our results show that genes in all three species cluster according to metabolic pathways, modules tend to have cell type specific expression patterns, and that modules in different species tend to include orthologues.  Our network comparison indicates changes in connectivity of core photosynthesis genes between species, suggesting alterations in the organization of photosynthetic networks in different origins of C₄ species.  Understanding transcriptional regulatory networks in plants will promote the understanding of complex metabolic pathways thus allowing us to manipulate them to create better crops.