The majority of plants use C₃ photosynthesis, but over 60 independent lineages of angiosperms have evolved the C₄ pathway. In most C₄ species, photosynthesis gene expression is compartmented between mesophyll and bundle-sheath cells. We performed DNaseI sequencing to identify genome-wide profiles of transcription factor binding in leaves of the C₄ grasses Zea mays, Sorghum bicolor, and Setaria italica as well as C₃Brachypodium distachyon. In C₄ species, while bundle-sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that influence gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C₄ photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C₄ photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.

ABA-mediated desiccation tolerance in P. patens depends on a trimodular protein kinase, found only in early land plants and aquatic algae, proposed to have faci

Plant peroxisomes are important components of cellular antioxidant networks, dealing with ROS generated by multiple metabolic pathways. Peroxisomes respond to environmental and cellular conditions by changing their size, number, and proteomic content. To investigate the role of peroxisomes in response to drought, dehydration and ABA treatment we took an evolutionary and comparative genomics approach. Colonisation of land required evolution of dehydration tolerance in the absence of subsequent anatomical adaptations. Therefore, the model bryophyte Physcomitrella patens, the model dicot Arabidopsis thaliana and wheat (Tricitcum aestivum), a globally important cereal crop were compared. Three sets of genes namely 'PTS1 genes' (a proxy for genes encoding peroxisome targeted proteins), PEX genes (involved in peroxisome biogenesis) and genes involved in plant antioxidant networks were identified in all 3 species and their expression compared under drought (dehydration) and ABA treatment. Genes encoding enzymes of β-oxidation and gluconeogenesis, antioxidant enzymes including catalase and glutathione reductase and PEX3 and PEX11 isoforms showed conserved up-regulation, and peroxisome proliferation was induced by ABA in moss. Interestingly, expression of some of these genes differed between drought sensitive and resistant genotypes of wheat in line with measured photosynthetic and biochemical differences. These results point to an underappreciated role for peroxisomes in drought response.

C ₄ photosynthesis has evolved by repurposing enzymes found in C ₃ plants. Compared with the ancestral C ₃ state, accumulation of C ₄ cycle proteins is enhanced. We used de-etiolation of C ₄ Gynandropsis gynandra and C ₃ Arabidopsis thaliana to understand this process. C ₄ gene expression and chloroplast biogenesis in G. gynandra were tightly coordinated. Although C ₃ and C ₄ photosynthesis genes showed similar induction patterns, in G. gynandra , C ₄ 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 C ₄ 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 C ₄ photosynthesis genes in C ₄ leaves is enhanced because modifications in cis allowed integration into ancestral transcriptional networks.